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1. Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification

   https://doi.org/10.1002/ajb2.16025  

   Murillo‐A, José; Valencia‐D, Janice; Orozco, Clara I; Parra‐O, Carlos; Neubig, Kurt M (July 2022, American Journal of Botany)

   Abstract PremiseTo date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target‐enriched nuclear data to improve our understanding of phylogenetic relationships in the family. MethodsWe used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species inBrunellia, and several outgroup taxa. We removed loci that indicated biased inference of relationships and applied concatenated and coalescent methods to inferBrunelliaphylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage sorting events and assessed their impact on phylogenetic inference. Finally, we performed ancestral‐state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections inBrunellia. ResultsBrunelliacomprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses. ConclusionsPhylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene‐tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character‐state reconstructions. While target enrichment data allows us to broaden our understanding of diversification inBrunellia, the relationships among subclades remain incompletely understood. 

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2. Geography and admixture shape the genome‐scale phylogeny of North American Delphinium

   https://doi.org/10.1111/nph.71042  

   Meek, Jared B; Cook, Daniel; Bushman, B Shaun; Thorsted, Kim; Eaton, Deren_A R (May 2026, New Phytologist)

   Summary The genusDelphiniumexemplifies the complexity of plant diversification in mountainous regions, where rapid speciation, hybridization, and morphological convergence frequently obscure species boundaries. The North American lineageDelphiniumsect.Diedropetalahas rapidly radiated across a range of ecological habitats, from alpine tundra to desert grasslands, forming an iconic component of western wild flower communities.Here, we present a genome‐scale phylogeny of 34 taxa using ddRAD‐seq data from 150 individuals sampled across their geographic ranges.Our results reveal strong phylogenetic structure corresponding to biogeographic regions, including several well‐supported clades that cut across existing taxonomic subsections, emphasizing the need for taxonomic revision. Hybridization and introgression are widespread, occurring both within and between these regional clades. Most species are connected through a syngameon‐like network of introgression, with few widespread species acting as central hubs. We describe six higher‐level clade names and use an agent‐based artificial intelligence analysis to identify morphological synapomorphies that align with our genomic findings.Our study demonstrates that geography and gene flow have played a dominant role in shaping the evolutionary history ofDelphiniumin North America, offering a framework for revising its taxonomy and informing future conservation efforts. 

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3. Phylogenetic relationships and the repeated loss of traits associated with sicklebill pollination in Centropogon subgenus Centropogon (Campanulaceae)

   https://doi.org/10.1002/ajb2.70016  

   Mansaray, Janet K; Bedoya, Ana M; Frost, Laura A; Degreenia, Olivia C; Lagomarsino, Laura P (March 2025, American Journal of Botany)

   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. 

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4. The unique morphological basis and repeated evolutionary origins of personate flowers in Penstemon

   https://doi.org/10.1002/ajb2.70078  

   Depatie, Trinity H; Wessinger, Carolyn A (August 2025, American Journal of Botany)

   Abstract PremiseAdaptive radiation in ecologically and morphologically diverse plant lineages presents an opportunity to investigate the rapid evolution of novel floral traits. While some types of floral traits, such as flower color, are well characterized, other types of complex morphologies remain understudied. One example is occluded personate flowers, dorsoventrally compressed flowers with obstructed floral passageways, which have evolved in multiple genera, but have only been characterized from snapdragon. MethodsOur study examined the morphological basis and evolutionary history of personate flowers in a clade ofPenstemonspecies that includes three personate‐flowered species. We characterized floral morphology and inferred phylogenetic relationships for 13 species in this group to examine the evolutionary history of personate flowers. We used phylogenomic tests for introgression to examine whether personate‐flowered lineages have a history of introgression. ResultsUnlike the personate flowers of snapdragon, personate flowers inPenstemonare produced by deep pleats in the ventral petal tissue that curve the ventral petal surface upward, obstructing the floral tube opening. Our phylogenetic tree suggests that personate flowers evolved in two separate lineages. Phylogenomic analyses indicate incomplete lineage sorting and introgression between certain taxa have contributed to phylogenomic discordance; however, we found little evidence of recent introgression between the two personate‐flowered lineages. ConclusionsPersonate flowers inPenstemonhave a different morphological basis than those in snapdragon. Personate flowers have evolved multiple times inPenstemonon a rapid evolutionary timescale. The source of genetic variation for repeated shifts may be de novo mutations or pre‐existing variants. 

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5. Revealing Speciation Mechanisms Across Endemic Southern Andean Lilies ( Phycella , Hippeastreae, Amaryllidaceae) in the Chilean Biodiversity Hotspot

   https://doi.org/10.1111/mec.70050  

   García, Nicolás; Fuentes‐Castillo, Taryn; Román, María José; Folk, Ryan A (September 2025, Molecular Ecology)

   Sork, Victoria L (Ed.)

   ABSTRACT Cryptic speciation, an endemic problem in biodiversity hotspots, arises as a result of an uncoupling among three processes: lineage splitting, morphological diversification, and ecological divergence during rapid speciation. We studied speciation processes inPhycella(Amaryllidaceae), a clade mostly restricted to the Chilean Biodiversity Hotspot, aiming to differentiate the relative roles of geographic and ecological speciation as well as the role of secondary gene flow in this radiation. We sampled a total of 137 individuals from 47 populations, including all described taxa throughout the geographic range of the group. Using 884 nuclear genes (1125 exons) and near‐complete plastomes through hybrid capture, we resolved the phylogeny ofPhycellawith high support and demonstrated substantial phylogenetic resolution at the population level. Analyses of niche overlap among species and nuclear clades suggest that the diversification ofPhycellawas associated with niche divergence, supporting a predominantly geographic mode of speciation in the group, likely driven by the mountainous landscape characteristic of the central area of the Chilean Biodiversity Hotspot. Phylogenetic network and modelling approaches identified major cytonuclear discord, attributable to proximity‐based secondary gene flow among species, largely restricted to cytoplasmic DNA. Finally, we present a major integrative taxonomic proposal that dividesPhycellainto 18 species on the basis of molecular, morphological, and ecological data. Overall, our results highlight the relevance of the mountainous landscape of central Chile to promote diversification inPhycella, and ours is among a few studies on speciation for an endemic element of the Chilean Biodiversity Hotspot. 

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