Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora.

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.

Phylogeny, classification, and character evolution of tribe Citharexyleae (Verbenaceae).

PREMISE: As a family of Neotropical origin and primarily Neotropical distribution, the Verbenaceae are a good but understudied system with which to understand Neotropical evolution. Tribe Citharexyleae comprises three genera: Baillonia, Citharexylum-one of the largest genera in Verbenaceae-and Rehdera. A molecular phylogenetic approach was taken to resolve intergeneric relationships in Citharexyleae and infrageneric relationships in Citharexylum. The phylogeny is used to elucidate character evolution in a widespread, morphologically diverse Neotropical genus. METHODS: Seven plastid regions, two nuclear ribosomal spacers, and six low-copy nuclear loci were analyzed for 64 species of Citharexyleae. Phylogenetic analyses were conducted using maximum likelihood, Bayesian inference, and multispecies coalescent approaches. Habit, presence or absence of thorns, inflorescence architecture, flower color, fruit color, and geography were examined to identify diagnostic character states for clades within Citharexylum. RESULTS: Rehdera is resolved as sister to Citharexylum, and Baillonia nested within Citharexylum. Two species, C. oleinum and C. tetramerum, are not closely related to tribe Citharexyleae, but may be related to members of tribe Duranteae instead. Seven clades within Citharexylum are inferred, each characterized by a combination of geography, fruit color and/or maturation, and inflorescence architecture. There is evidence of correlated evolution between habit, axillary inflorescences, and flower number per inflorescence. Shrubs with reduced inflorescences have evolved repeatedly. CONCLUSIONS: A subgeneric classification for Citharexylum is proposed. Although suites of associated traits are found, character morphology has been labile throughout Citharexylum's evolutionary history. Morphological diversity may be related to adaptation to differing mesic and xeric habitats.

Origins of North American arid-land Verbenaceae: More than one way to skin a cat.

PREMISE OF THE STUDY: Verbenaceae originated and initially diversified in South America in wet forest habitats. They have diversified extensively in arid habitats in both South and North America. This study aims to understand the origin of the North American arid-land members of Verbenaceae. METHODS: A phylogenetic approach is used to examine four genera (Aloysia, Citharexylum, Glandularia, Verbena) in three distinct clades with representatives in North American deserts and disjunct South and North American distributions. Phylogenetic analyses were conducted using maximum likelihood and Bayesian approaches. Analyses included both plastid and nuclear DNA regions and include the first study of Citharexylum and an expanded sampling of tribe Verbeneae (Glandularia and Verbena). Ancestral areas were reconstructed for each group. KEY RESULTS: North American desert species of Aloysia and Glandularia were likely derived from ancestors in arid temperate South America, perhaps by long-distance dispersal. The pattern for Verbena was less clear, with evidence from plastid DNA implicating an Andean dispersal route to the North American clade, whereas nuclear data suggest that the Andean and North American species resulted from independent dispersals from southern South America. A previously unrecognized clade of Andean Verbeneae was discovered, raising the possibility of an Andean origin of Verbena or Verbena and Glandularia. North American desert species of Citharexylum represent multiple, independent origins from mesic habitat ancestors in Mesoamerica. CONCLUSIONS: North American arid-zone Verbenaceae are derived from South and Central American ancestors via multiple avenues, including long-distance, amphitropical dispersal, Andean migration corridors, and in situ evolution of desert-adapted species.