Pamela Sue Soltis

Sapotaceae are a pantropical family of woody plants whose trees often dominate tropical forests. Despite their diversity and ecological importance, only a rudimentary understanding of their phylogeny and biogeographic history is available. In this study, we aim to construct a well-sampled and robust phylogeny for Sapotaceae, investigate their biogeographical history, and identify current knowledge gaps using species distribution data. We generated and dated phylogenetic trees using both nuclear and plastome genomic sequence data, assessed conflict between gene-trees and species-trees, and conducted historical biogeographic analyses. Nuclear and plastome datasets recovered clades that correspond to the previously described subfamilies within Sapotaceae. However, we observed significant conflict between the nuclear and plastome phylogenies and among individual nuclear gene trees. Such conflict could result from the fact that plants of Sapotaceae species are, in general, long-lived, and the nuclear genome may be more greatly impacted than the plastome by evolutionary processes such as hybridization and incomplete lineage sorting. We suggest that these processes may limit the resolving power of nuclear data in Sapotaceae phylogenetics, and that plastome data should be used together with nuclear data for resolving evolutionary relationships. We recovered two main Neotropical clades for the subfamily Chrysophylloideae, a novelty for Sapotaceae. Ancestral range estimation based on nuclear data suggests an East Asian origin for Sapotaceae, although the plastome-based analysis presents disagreement. Finally, our results highlight the need for increased sampling and research on Australasian species, which remain underrepresented in current datasets.

We present here a revision of the APG classification that considers the extensive recent analyses of hundreds of nuclear and plastid genes for many angiosperm species. Although previous versions of the APG classification were largely based on uniparentally inherited markers (plastid DNA, typically maternally inherited), there has emerged since APG IV extensive evidence of widespread hybridization and inheritance of ancestral polymorphisms. Despite this evidence of gene‐tree discordance, most of the APG IV classification is supported by both plastid and nuclear analyses, and only a few revisions are required in this update to make the classification parallel phylogenetic results in the literature. At the ordinal level, few changes in circumscription are required relative to the last APG version, although the fabids now comprise only the four nitrogen‐fixing orders (Cucurbitales, Fabales, Fagales, and Rosales) and the malvids now include the former COM clade (Celastrales, Malpighiales, and Oxalidales), which, in nuclear DNA analyses, is no longer monophyletic. Oncothecales (with only Oncothecaceae) and Cardiopteridales (with Cardiopteridaceae and Stemonuraceae) are newly recognized, and Icacinales are restricted to Icacinaceae. Restriction of Aquifoliales and Bruniales to just Aquifoliaceae/Helwingiaceae and Bruniaceae, respectively, is also proposed. Huaceae and Columelliaceae are unplaced to order among the malvids and campanulids, respectively. At the family level, expanded circumscriptions include Tecophilaeaceae (including Ixioliriaceae, Asparagales), Frankeniaceae (including Tamaricaceae, Caryophyllales), Phytolaccaceae (including Agdestidaceae and Sarcobataceae, Caryophyllales), Helwingiaceae (including Phyllonomaceae, Aquifoliales), Gesneriaceae (including Calceolariaceae and Peltantheraceae, Lamiales), Pentaphylacaceae (including Sladeniaceae, Ericales), and Orobanchaceae (including Mazaceae, Paulowniaceae, Phrymaceae, and Wightiaceae, Lamiales). In Santalales, the limits of Santalaceae and Olacaceae are revised, and Erythropalaceae and Strombosiaceae are recognized as distinct from Olacaceae; Balanophoraceae are maintained as distinct from Santalaceae, but this is a tentative placement. Generic relationships in Dioscoreales require more analyses before a revised family classification can be proposed, so we maintain the APG IV families of this order.

Rhexia (Melastomataceae), a temperate genus composed of 13 species in eastern North America, provides a useful system for evaluating how taxonomic and cytogenetic complexity influence forecasts of climate-driven habitat suitability distribution. Ecological niche models incorporating climatic and edaphic variables were used to estimate current and future habitat suitability for diploid, polyploid, and mixed-cytotype species. Habitat suitability was strongly associated with soil texture, hydrological conditions, and precipitation, with suitable environments characterized by sandy, acidic, and seasonally moist habitats. Projections under future climate scenarios revealed highly variable, species-specific responses, with some taxa exhibiting substantial expansions in the distribution of suitable habitat and others experiencing pronounced contractions. Contrary to expectations, ploidal level was not consistently associated with niche breadth or climate response, as both diploid and polyploid species displayed a wide range of outcomes. These findings highlight the need for flexible, habitat-focused conservation strategies that consider hydrological and edaphic variables and demonstrate how taxonomic and cytogenetic complexity can complicate forecasts of biodiversity change under future climate scenarios.

Whole-genome duplication (WGD), or polyploidy, is a major evolutionary force throughout the tree of life. Ancient WGDs are commonly inferred from the distribution of synonymous substitutions per synonymous site ( K _s ) between duplicated genes. Here, we argue that the standard interpretation of these distributions is incomplete. Using haplotype-phased genome assemblies spanning canonical autopolyploid and allopolyploid systems, we find that K _s accumulates primarily between gene copies on non-recombining chromosomes. Thus, K _s -based WGD detection depends not simply on WGD, but on whether duplicated copies evolve independently. This distinction reframes many inferences of ancient WGD as signatures of hybridization and the evolution of meiotic isolation and alters how we interpret the origin, detectability, and evolutionary consequences of polyploidy across the tree of life. Significance: Whole-genome duplication (WGD) is prevalent across the tree of life, and its signatures appear in nearly every sequenced genome. Here we show that the predominant gene-based approach for detecting ancient WGD events is biased towards allopolyploid events arising through hybridization. The current approach is poorly suited to detecting WGD that occurs within a single species, also known as autopolyploidy. These findings suggest we likely underestimate the frequency of ancient polyploids. Furthermore, most signals of ancient WGD may therefore record not only genome doubling, but also the merger of previously divergent evolutionary lineages. Overall, our results suggest that the paleopolyploidy record inferred from current methods is an incomplete account of WGD and reveals deep hybridization preserved in eukaryotic genomes.

Extinction has received considerable attention in animals, particularly charismatic vertebrates. Plants, like animals, face alarming extinction risks with many of the same underlying causes including habitat loss, climate change, disease, invasive species, and over harvesting. However, habitat modifications by humans might make it much more challenging for plants to respond to rapid contemporary climate change by shifting distributions, either because suitable habitat no longer exists or because the human-altered landscapes pose too great a barrier to dispersal for some species. De-extinction (i.e. the revival of genes or phenotypes of extinct species) has similarly received considerable attention in animals with little discussion in plants. De-extinction is already possible in plants, particularly for those species with close relatives for which there are rich genomic resources as well as the capacity for CRISPR-mediated gene editing and regeneration. Herbarium collections offer one important source of DNA for plants that have gone extinct in recent centuries. The opportunities for de-extinction in plants will only increase as genomic resources and the tools for regeneration and genome editing improve. We also consider some of the ethical issues related to de-extinction in plants, focusing our discussion of the topic to those plants clearly driven to extinction by human activity in just the past few hundred years.

Carya glabra (2n = 4x = 64), also known as pignut hickory, is a widely distributed species in the walnut family (Juglandaceae). Native to the central and eastern United States and southeastern Canada, C. glabra plays an important ecological role as a common upland forest species; it is closely related to several economically valuable nut trees, including Carya illinoinensis (pecan). A deeper understanding of the genetics of C. glabra is essential for studying its evolutionary history and biology, with potential implications for agricultural improvement of pecan. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome level and phased, representing the first assembled polyploid genome in the genus Carya. A total of 64 pseudochromosomes were assembled and phased into 4 haplotypes. The haplotype A assembly spans 600.4 Mb, comprises 55.0% repetitive sequences, and contains 30,947 protein-coding genes, with a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 97.7%. Functional annotation assigned 94.3% of haplotype A genes to gene families, and 79.7% and 86.3% of genes were annotated with Gene Ontology terms and protein domains, respectively; 635 putative plant disease resistance genes were found in haplotype A. The other 3 haplotypes exhibited similarly high-quality annotation metrics. Our genomic analyses also suggest that C. glabra is an autotetraploid. Comparative genomic analyses revealed high collinearity among the 4 haplotypes of C. glabra and the published genomes of 3 other Carya species, although structural variation among the genomes of these species was identified. In addition, we provide an improved chloroplast genome assembly and the first mitochondrial genome for C. glabra. We also provide a phylogenomic tree for Carya based on numerous nuclear genes, showing that C. glabra forms a clade with other North American tetraploid species. Importantly, most members of the research team are undergraduate students; the sequenced individual is located in McCarty Woods, a Conservation Area on the University of Florida campus. This work highlights the value of genome assembly efforts as powerful tools for teaching genomics and supporting conservation initiatives. This first high-quality reference genome for C. glabra provides a valuable resource for studying Carya, a genus of significant ecological and economic importance.

Aim: The assembly of tropical tree floras is complex, involving many lineage‐specific histories; however, focusing on the biogeographic history of diverse clades can reveal general patterns. We investigated the historical biogeography of the ecologically important Brazil nut clade (Lecythidoideae) to: (1) expand prior phylogenies with greater sampling of the early branching Andean‐centered subclades; (2) infer the ages and dispersal histories of the major subclades; and (3) document instances of niche evolution within Lecythidoideae, with an emphasis on elevational range shifts. Location: Tropical America. Taxon: The Neotropical subfamily Lecythidoideae (Lecythidaceae). Methods: We expanded phylogenetic taxon sampling to 371 samples representing 197 species across bioregions, emphasizing the Andean‐centered genera Grias and Gustavia . A maximum likelihood phylogeny was inferred using 665 nuclear loci, and divergence times were estimated with four fossil constraints. Ancestral ranges were reconstructed across bioregions and ecoregions using three biogeographic models. Results: The crown age of Lecythidaceae is placed in the mid‐Cretaceous (~94 Ma) and the Neotropical clade Lecythidoideae in the Eocene (~51.5 Ma). Grias likely originated in Central America or the Pacific coastal forests of South America (~35.5 Ma), Gustavia in the Amazonian moist forests (~36 Ma) and the Bertholletia clade in Western‐Central Amazonia (~20 Ma). Following geographic dispersal from eastern and western sources, Grias , Gustavia and Lecythis diversified along the Andean slopes; Scottmoria in Central America, and Imbiriba in the Atlantic Forest. Main Conclusions: Most Lecythidoideae subclades diversified during the Miocene, a period of major landscape change associated with the tectonic activities that generated the Northern Andes, the formation of the Amazon drainage system and the closure of the Isthmus of Panama. While most species retained lowland rainforest niches, several lineages shifted into Andean montane forests, highlighting how geological change and ecological transitions shaped the assembly of Neotropical tree floras.