Ana Maria Bedoya

Premise: The species‐rich flora of Tropical Andes underwent multiple rapid and recent diversifications, yet resolving their evolutionary histories remains challenging despite increasing phylogenomic data. Here, we examined phylogenomic conflict in Brachyotum (Melastomataceae) to identify sources preventing its resolution. Methods: We sequenced multiple nuclear loci through target capture and plastid loci through genome skimming for approximately two thirds of Brachyotum species. We analyzed nuclear loci with concatenated maximum‐likelihood, multispecies coalescent (MSC), and phylogenetic network approaches, whereas plastid loci were analyzed with a concatenated maximum‐likelihood. Results: Topological conflict was widespread among gene trees. Brachyotum was inferred as monophyletic by concatenated nuclear and ASTRAL approaches, but as paraphyletic by BEAST and phylogenetic network analyses, the latter involving four introgression events. Plastid analyses also recovered paraphyly. Across analyses, the backbone of Brachyotum showed low branch support, and individual nuclear loci yielded markedly divergent topologies across inference methods. Conclusions: Despite pervasive gene tree discordance, the signal for multiple introgression events is robust. Cytonuclear discordance between plastid and nuclear data further supports introgression. Our results suggest that current phylogenomic approaches may not fully capture the evolutionary complexity of Brachyotum , a challenge that may extend to other rapid Andean plant radiations.

Aim: Biological and geographic patterns and processes are linked such that biological data hold information on paleogeographical patterns and processes. Here, we aimed to test Biogeographic dating as a methodological framework for the integration of biological, paleontological and geological data to test paleogeographic hypotheses. In doing so, we test the potential for well‐calibrated phylogenies and the impact of accuracy and uncertainty in geological priors for estimating paleogeographic events. Location: Global. Time Period: Various scales. Taxa: Flora and Fauna. Methods: We investigate the interaction of biological and paleogeographic data and priors in Biogeographic dating, where both are specified and analyzed simultaneously. We evaluate how uncertainty and accuracy in both types of datasets affect the inference of divergence times used as a proxy for generating or testing geological models. We used data simulation to generate a paleogeographic scenario and a nuclear sequence dataset for lineages whose evolution is correlated with geological patterns. Then, gene flow was simulated across landscape units, such that biological patterns inferred from sequence data would deviate from simulated times of paleogeographic change. Under those two scenarios, we specified broad, incorrect and accurate geological priors. These various scenarios were analyzed through Biogeographic dating analyses run in RevBayes and compared with our simulations. Results: Models with flat paleogeographic priors (unknown geological models or lack of geological data) were able to accurately infer node dates when simulated biological data mirrored the pattern and timing of paleogeographic events. Gene flow results in divergence time estimates that deviate from the simulated scenario. Our findings also underscore the limitations and sources of error in the use of Biogeographic dating for informing species divergence times and paleogeographic models. Conclusions: Our results indicate that Biogeographic dating is a plausible methodological framework for empirical studies integrating biological and geological data to test landscape change scenarios. However, caveats inherent to model assumptions and specifications that result in older estimated divergence times should be taken into account when interpreting results. Implementation of this framework should be coupled with the selection of good biological study systems, achieved through the careful study of focal clades.

A bstract: Hillieae is a group of ∼30 florally diverse, Neotropical epiphyte species. Species richness peaks in southern Central America and taxa display bat, hawkmoth, or hummingbird pollination syndromes. A phylogenetic framework is needed to understand floral and biogeographic evolution. We used target enrichment data to infer a species tree and a Bayesian time-calibrated tree including ∼83% of the species in the group. We inferred ancestral biogeography and pollination syndromes, described species realized bioclimatic niches via a principal component analysis, and estimated significant niche shifts using Ornstein-Uhlenbeck models to understand how different abiotic and biotic variables have shaped Hillieae evolution. We estimated that Hillieae originated in southern Central America 19 Ma and that hawkmoth pollination is the ancestral character state. Multiple independent shifts in pollination syndrome, biogeographic distribution, and realized bioclimatic niche have occurred, though bioclimatic niche is largely conserved. Using generalized linear models, we identify two interactions— between species’ biogeographic ranges and pollination syndromes, and between phylogenetic covariance and pollination syndromes— that additively affect the degree of bioclimatic niche overlap between species. Regional variation in pollination syndrome diversity and patterns of species bioclimatic niche overlap indicate a link between biogeography and species ecology in driving Hillieae diversification and syndrome evolution.

Premise: Centropogon subgenus Centropogon comprises 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.Methods: We 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.Results: We 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, with C. cornutus forming a clade and C. granulosus and C. solanifolius forming non‐monophyletic, biogeographically clustered lineages. Correlated evolution of floral curvature and inflorescence structure has led to multiple putative losses of sicklebill pollination.Conclusions: Centropogon subgenus Centropogon adds 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.

Premise: Seed dispersal is a critical process impacting individual plants and their communities. Plants have evolved numerous strategies and structures to disperse their seeds, but the evolutionary drivers of this diversity remain poorly understood in most lineages. We tested the hypothesis that the evolution of wind dispersal traits within the melicgrasses (Poaceae: Meliceae Link ex Endl.) was correlated with occupation of open and disturbed habitats.Methods: To evaluate wind dispersal potential, we collected seed dispersal structures (diaspores) from 24 melicgrass species and measured falling velocity and estimated dispersal distances. Species’ affinity for open and disturbed habitats were recorded using georeferenced occurrence records and land cover maps. To test whether habitat preference and dispersal traits were correlated, we used phylogenetically informed multilevel models.Results: Melicgrasses display several distinct morphologies associated with wind dispersal, suggesting likely convergence. Open habitat taxa had slower‐falling diaspores, consistent with increased wind dispersal potential. However, their shorter stature meant that dispersal distances, at a given wind speed, were not higher than those of their forest‐occupying relatives. Species with affinities for disturbed sites had slower‐falling diaspores and greater wind dispersal distances, largely explained by lighter diaspores.Conclusions: Our results are consistent with the hypothesized evolutionary relationship between habitat preference and dispersal strategy. However, phylogenetic inertia and other plant functions (e.g., water conservation) likely shaped dispersal trait evolution in melicgrasses. It remains unclear if dispersal trait changes were precipitated by or predated changing habitat preferences. Nevertheless, our study provides promising results and a framework for disentangling dispersal strategy evolution.

Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well‐known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long‐standing questions on how the earth evolved with the use of plant DNA.

Premise: Rubiaceae is among the most species‐rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large‐scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single‐copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae‐specific probe set that allows for comparable phylogenetic inference across clades is lacking.Methods: Here, we use publicly accessible genomic resources to identify putatively single‐copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent‐aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae.Results: We recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance.Discussion: Our probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.

Two species of Podostemaceae, with few previous georeferenced records West of the Andes in northern South America, are reported across the Andes in the region. Our records document a wider range of the Podostemaceae in the tropical Andes and result from recent floristic explorations in Andean rivers in Ecuador and Colombia. These new records are of use for future research in the group, as well as for conservation projects in rivers. We call for international collaborative projects supporting local collectors and institutions in Latin America to bolster research in the under-collected river plants and assess their distribution. We extend the invitation to local scientists to get their feet wet and collect plants in river-rapids and waterfalls.

Summary: Northern South America is a geologically dynamic and species‐rich region. Fossil and stratigraphic data show that mountain uplift in the tropical Andes reconfigured river drainages. These landscape changes shaped the evolution of the flora in the region, yet the impacts on aquatic taxa have been overlooked. We explore the role of landscape change on the evolution of plants living strictly in rivers across drainage basins in northern South America by conducting population structure, phylogenetic inference, and divergence‐dating analyses for two species in the genus Marathrum (Podostemaceae). Mountain uplift and drainage basin formation isolated populations of M. utile and M. foeniculaceum in northern South America and created barriers to gene flow across river drainages. Sympatric species hybridize and the hybrids show the phenotype of one parental line. We propose that the pattern of divergence of populations reflects the formation of river drainages, which was not complete until < 4.1 million yr ago (Ma). Our study provides a clear picture of the role of landscape change on the evolution of plants living strictly in rivers in northern South America. By shifting the focus to aquatic taxa, we provide a novel perspective on the processes shaping the evolution of the Neotropical flora.