Christine D. Bacon

Mitochondrial genomes of angiosperms are unusual due to their large size, low gene content, and high structural variation. In the palm family (Arecaceae), mitochondrial architecture is highly dynamic, characterized by expansive sizes, fragmentation, and extensive recombination activity. This biological complexity presents a significant bioinformatic challenge, especially since only three complete palm mitochondrial genomes are publicly available to date. Here, we present the complete mitochondrial genome sequence for the Amazonian palm Euterpe precatoria , assembled de novo using PacBio HiFi long-read sequencing data. The assembly required extensive manual curation and graph tracing to resolve a complex recombination topology. The final resolved sequence spans 1,268,308 base pairs and is supported by a mean read coverage depth estimated at 746X. Annotation revealed a high degree of structural complexity, including 177 total gene features corresponding to 76 unique genes. This gene set includes 41 unique protein-coding genes (56 features), 32 unique tRNA genes (118 features), and three unique rRNA genes, reflecting the characteristic gene duplication and fragmentation documented in Arecaceae. The complete mitochondrial genome sequence is publicly available and provides a high-quality resource for understanding the mechanisms of plant mitochondrial genome expansion and structural evolution.

Global temperatures have risen ~ 1.1°C since the 1800s and the mean annual air temperature in the Arctic has increased by nearly four times the global average. Temperature has a significant effect on fundamental life‐cycle events of flora and fauna. With temperatures increasing, Arctic plants are expected to shift their active periods accordingly, with a shorter flowering period as later flowering plants converge with flowering timing of early flowering plants. Nearly 120 years of herbarium records and collection data were leveraged to identify flowering shifts in the Arctic–alpine plant Oxyria digyna using climatic data and linear regressions. We found that alpine, boreal Arctic, and Arctic tundra populations of Oxyria digyna differed in their flowering time response to increased air temperature. The boreal Arctic population showed a significant advancement in flowering time as related to mean summer and June temperature increases, while the flowering time of Arctic tundra and alpine populations had a shift in flowering timing in response to June temperature change. Our results identify biodiversity response to climate change and determine which populations have greater adaptive potential to respond to rapidly changing abiotic conditions in the Arctic and beyond.

Caviomorph rodents diversified widely in the Americas. Within this group, the sister clades Octodontoidea (spiny rats and allies) and Chinchilloidea (chinchillas and allies) illustrate strikingly imbalanced evolution, with 195 extant species in the former and only six in the latter. Fossil evidence, however, documents greater past diversity and disparity in Chinchilloidea, including the largest known rodents. Here, we integrate data from extant and extinct species to investigate how evolutionary dynamics shaped these contrasting trajectories. Using a phylogenetic framework, we reconstructed patterns of body mass and craniodental evolution. The ancestral body mass was small, but Chinchilloidea expanded into a broader size range, showing significantly higher rates of body mass evolution than Octodontoidea. Subsequent Neogene and Quaternary extinctions erased much of this variation, reversing a ~30 million-year trend of greater body mass disparity. Craniodental disparity, however, followed a different trajectory: initially higher in Chinchilloidea, it later became greater in Octodontoidea after the Miocene. Importantly, craniodental disparity remained relatively stable in both clades despite major diversification and extinction events. These findings highlight the decoupling of taxonomic diversity, body mass and craniodental morphology, underscoring the complexity of evolutionary dynamics even for sister clades that evolved on the same continent.

Predation is a key driver of speciation and phenotypic diversification, yet how antipredator traits evolve and persist over evolutionary time remains poorly understood. We generated target sequence capture and whole-genome sequencing data for the skipper butterfly subfamily Eudaminae (Hesperiidae) to test whether antipredator defenses, in interaction with environmental variation, promote diversification. We focus on two antipredation wing traits: hindwing tails, which deflect predator attacks, and blue-green coloration, which may enhance motion dazzle and be used as warning coloration. Applying phylogenomics, morphometrics, and comparative methods, we model trait evolution in relation to diel activity and geographic distribution and find that hindwing tails repeatedly evolved at least seven times and blue-green coloration at least fifteen times. Both traits are associated with elevated speciation rates, but evolutionary transitions toward tailless wings and non-iridescent coloration occurred more frequently than trait gains, indicating high evolutionary lability of these antipredator defenses. Trait loss, particularly pronounced in tropical diurnal species, may reflect trade-offs in flight performance, shifts in predation guilds, or the evolution of alternative defensive traits. Our findings highlight rampant convergent evolution of wing traits that are under strong predator-mediated selection. By identifying how antipredator defenses and environmental contexts influence phenotypic and species diversification, this study provides new insights into the ecological and evolutionary processes underlying insect diversity.

The palm family (Arecaceae) has a rich history of phylogenetic research, including several recent phylogenomic studies. However, densely sampled phylogenomic datasets for larger palm clades – such as subfamilies – are still few in number. We used target sequence capture to obtain data for 971 nuclear genes across 421 (ca. 80%) species in the subfamily Coryphoideae. We inferred a robust phylogenetic tree to address systematic issues in the subfamily, specifically the relationships among tribes Cryosophileae, Sabaleae, Phoeniceae and Trachycarpeae, the affinities of seven genera in Trachycarpeae that are not currently assigned to any subtribe, and the monophyly of genera across the subfamily. We recovered relationships among tribes that are in accordance with other major nuclear phylogenomic datasets, but that are incongruent with trees derived from plastome sequences. Importantly, the placement of tribe Phoeniceae (the date palms) remains contentious. Our tree recovered with high support the relationship of all unplaced Trachycarpeae genera, paving the way for an updated classification. Most genera were resolved as monophyletic except for Livistona and all three genera of tribe Caryoteae, calling for a revision of generic limits. Our tree clarifies the relationships of many fan palm species for the first time, allowing for future studies of diversification, trait evolution or biogeography.

Two species of Iriartella were recognized in the most recent revision of the genus. Molecular data appeared to show that only one species should be recognized. However, an analysis of the molecular data, together with examination of morphological data from herbarium specimens, appears to support the recognition of two species.

Premise: Species complexes are groups of closely related species with ambiguous delimitation, often composed of recently diverged lineages. Polyploidization and uniparental reproduction (i.e., selfing and apomixis) can play important roles in the origin of species complexes. These complexes pose challenges for species‐based scientific questions, such as the estimation of species richness or conservation prioritization.Methods: We determined the potential of resolving taxonomically complex groups using target enrichment in the circumpolar Silene uralensis complex (Caryophyllaceae). We proposed a metric using genetic distances between phased alleles to distinguish diploids from allopolyploids.Results: Our results identified geographic structure of populations, with the northern American and Greenlandic samples having a common ancestor. We found little phylogenetic support for the most recent taxonomic treatment of the Silene uralensis complex.Conclusions: The study highlights the use of target enrichment in testing taxonomic hypotheses in diploids and the challenges of studying recently diverged lineages.

Senna sect. Chamaefistula ser. Coriaceae is restricted to Brazil and is predominantly distributed in savanna habitat. The species are morphologically characterized by their shrub or treelet habit, usually reniform stipules, extrafloral nectaries usually positioned on the middle or distal part of the petiole, zygomorphic corolla and laterally compressed fruits with the seeds parallel to the fruit valves. Previous taxonomic studies have recognized only three species and one variety, nevertheless, they provided the groundwork for a more comprehensive treatment, presented here. Based on fieldwork and on the analysis of herbarium specimens, we recognize five species belonging to Senna ser. Coriaceae including one new species from the seasonally dry areas in the Chapada Diamantina, Senna diamantinensis. We carried out a morphometric analyses and here recognize S. caesia as a distinct species rather than a variety of S. corifolia. We propose a new combination for Cassia kuhlmannii and recognize it under the genus Senna. In addition, we propose two first-step lectotypifications and one second-step lectotypification. The taxonomic treatment provided here includes an identification key, morphological descriptions, taxonomic notes, illustrations, preliminary conservation assessments, and habitat and phenology data for each species.

The Neotropics have been host to a myriad of geological and climatic events that have shaped the biodiversity present in the region. Bromeliaceae forms one of the most prominent components of the Neotropical flora, being considered the largest group nearly exclusive to the Americas, with almost 4000 species divided into eight subfamilies. Here, we utilize a new time-calibrated molecular phylogeny including 1268 bromeliad taxa and integrate habitat and morphological data to answer the following questions: (i) Are bromeliad subfamilies monophyletic, and did Neogene and Quaternary events in South America coincide with their divergence? (ii) Did naked seeds of berry-fruited species, epiphytic growth, and climatic factors increase bromeliad diversification? Our analysis reconstructed a new topology concerning some recently diverged lineages, with the genus Bromelia emerging as the sister group of a clade including all remaining Bromelioideae lineages + Puyoideae. Miocene events possibly triggered the diversification of bromeliads after a long period of stasis during the Palaeogene. We hypothesize that the morphological shift between Bromelia and Bromelioideae (except Bromelia) is related to the colonization of a new high-elevation environment by Puyoideae in the Andes. Additionally, our results show that naked seeds and the epiphytic growth form positively influence diversification rate, while precipitation, temperature, and elevation have a negative influence. We emphasize the importance of considering a variety of morphological and ecological features to enhance our understanding of bromeliad evolution.

Abstract— The genus Genipa is a widespread, lowland, Neotropical lineage of trees in the coffee family, Rubiaceae. There is long-standing disagreement on the delimitation of species in the genus and how broadly Genipa is circumscribed. Here, we use genomic data to resolve the classification within Genipa. Using target sequence capture we generated a high-resolution 245-locus dataset to produce a comprehensive species phylogeny under the multi-species coalescent model. The phylogenomic results strongly support Genipa spruceana, often synonymised with Genipa americana, as a distinct monophyletic species. Similarly, the monophyly of Genipa infundibuliformis, a recently recognized species, is also strongly supported. The phylogeny also shows three distinct, well-supported clades within the widespread species, Genipa americana. These clades are interpreted as three independently evolving lineages in contrast to the two varieties most commonly recognized in G. americana based on previous morphological studies.