Chelsea Dvorak Specht

Bulbostylis is the second‐most species‐rich genus in Abildgaardieae, comprising c. 221 species with a pantropical to warm‐temperate distribution and a remarkable ecological and morphological diversity. Despite advances in molecular phylogenetics confirming its monophyly, relationships within Bulbostylis remain poorly resolved, and previous attempts at creating infrageneric classifications are either geographically restricted or unsupported by phylogenetic evidence. Previous molecular studies have sampled fewer than 20% of the species of the genus, limiting our understanding of its evolutionary history. Here, we investigate relationships among 149 species and 3 subspecies of Bulbostylis , representing 69% of global diversity, using a universal probe kit for targeted genomic sequencing of flowering plants (Angiosperms353 probe kit). Our sampling also includes the genus Nelmesia , which we found to fall within Bulbostylis . We propose a new infrageneric classification and suggest a set of diagnostic morphological characters. Our revised infrageneric classification for Bulbostylis includes 18 sections and 8 subsections, providing a foundation for future taxonomic and evolutionary studies of this ecologically important genus.

Understanding crop genetic diversity is essential for conservation and breeding, yet farmer‐maintained germplasm remains largely underrepresented in genomic studies. Theobroma cacao L. has a complex domestication history, extensive global diversity, and is currently cultivated in Central America. Costa Rican cacao has been understudied compared to South American and Mexican cultivars despite cultural and historical importance. In this study, we investigate the genetic diversity of cacao from farmer‐managed systems across Costa Rica to search for Criollo germplasm while identifying and characterizing unique local genetic groups. Ninety‐four trees were sampled for whole genome resequencing from 17 farms across four regions of the country. Farmer materials were analyzed alongside 166 previously characterized reference accessions representing major cacao genetic groups. Population structure analyses, phylogenetic reconstruction, and network approaches revealed that Costa Rican cacao encompasses multiple known genetic groups, including Criollo‐derived lineages while also harbouring locally distinct diversity not represented in current global reference collections. Analyses revealed close kinship between many accessions with no clear geographic patterns corresponding to the observed population differentiation, reflecting the influence of farmers in generating the dominant patterns of gene flow through seed‐saving, clonal propagation, and sharing of genotypes among farms. Heterozygosity levels varied substantially among individuals, consistent with a mixture of highly inbred Criollo trees and more heterozygous, admixed genotypes. We find that farmer‐managed cacao systems are reservoirs of genetic diversity that can include rare or historically important lineages, underscoring the value of these farming systems for effective conservation and management of genomic resources for cacao resilience and improvement.

Background and Aims: Hybridization is a major driver of plant diversity, yet the role of cytogenetic compatibility, particularly differences in chromosome number, remains poorly understood. Differences in parental chromosome number can present barriers to hybrid formation by disrupting meiotic stability, but the extent to which biological and ecological factors influence the chromosomal architecture of hybrids remains poorly quantified, especially in monocots. This study aims to investigate how chromosome-number divergence interacts with biological and ecological factors to shape hybrid formation in monocots, using a novel quantitative metric, the Ploidy Deviation Index (PDI), to standardize comparisons of hybrid cytogenetic architecture. Material and Methods: We developed and applied the PDI, a continuous index quantifying chromosome-number deviation between a hybrid and its two parents, across approximately 200 hybrid cases with documented parental karyotypes. Hybrids were categorized as homoploid, uniparentally homoploid, intermediate or polyploid based on their PDI values. We analysed the distribution of PDI scores in relation to type of hybrid origin (natural vs. artificial), growth habit, size of the genus (a proxy for richness) and range of chromosome number within a genus (proxy for diversity). Comparisons across categories employed Anderson–Darling k-sample tests, multinomial logistic regression and Mann–Whitney U tests to determine significance. Key Results: Homoploid hybrids were found to be the most frequent. We found no significant difference in PDI distributions between natural and artificial hybrids. Significant variation in PDI distributions was found among growth habits, with aquatic hybrids more likely to be homoploid and geophytic hybrids showing higher proportions of polyploidy. Intermediate hybrids were common in larger genera with broader chromosome-number ranges, whereas polyploid hybrids showed the highest PDI values in large and karyotypically diverse genera. Conclusion: These results challenge long-held assumptions that polyploidy dominates hybrid formation and reveal that homoploid and intermediate chromosomal configurations are common in monocots. The PDI framework offers a powerful, standardized approach for assessing cytogenetic constraints on hybridization, with implications for systematics, evolutionary biology and conservation.

Understanding crop genetic diversity is essential for conservation and breeding, yet farmer-maintained germplasm remains largely underrepresented in genomic studies. Theobroma cacao L. has a complex domestication history and extensive global diversity, and cacao currently cultivated in Central America, particularly in Costa Rica, has been understudied compared to South American and Mexican cultivars despite cultural and historical importance. In this study, we investigate the genetic diversity of cacao from farmer-managed systems across Costa Rica to search for Criollo germplasm and identify and characterize any unique local genetic groups. Ninety-four trees were sampled from 17 farms across four regions of the country and sequenced using whole genome resequencing. Farmer materials were analyzed alongside 166 previously characterized reference accessions representing major cacao genetic groups. Population structure analyses, phylogenetic reconstruction, and network approaches revealed that Costa Rican cacao encompasses multiple known genetic groups, including Criollo-derived lineages, while also harboring locally distinct diversity not fully represented in current global reference collections. Analyses revealed close kinship between many accessions with no clear geographic patterns corresponding to the observed population differentiation, reflecting the effects of farmers in creating dominant patterns of gene flow through seed-saving, clonal propagation, and sharing genotypes among farms. Heterozygosity levels varied substantially among individuals, consistent with a mixture of highly inbred Criollo trees and more heterozygous, admixed genotypes. We find that farmer-managed cacao systems are reservoirs of genetic diversity, including possibly rare or historically important lineages, underscoring the value of these farming systems for effective conservation and management of genomic resources for cacao resilience and improvement.

Secondary vascular growth is a conserved mechanism that gives rise to vascular tissues produced via a single vascular cambium. Molecular mechanisms underlying this process are characterized mainly in model species with typical vascular architectures, while the genetics underlying ecologically-important atypical vascular architectures remain unexplored. We use developmental anatomy, comparative transcriptomics, molecular evolutionary analyses, and heterologous gene expression to address this knowledge gap, investigating how multiple ectopic cambia (EC) form in the woody vine Japanese wisteria. Anatomical studies show EC in Japanese wisteria arise from cortical parenchyma, and cambium-specific transcriptome comparisons reveal that genes acting as regulators of typical cambium development in model species are likewise associated with EC development. Gene trees of KNOX genes suggest that duplication events may contribute to EC formation, including a Fabaceae-specific duplication of KNAT2/6, which is detected as being under positive selection. We also demonstrate that KNOX genes from Japanese wisteria show canonical KNOX-like activity in heterologous functional assays, although no vascular aberrations were observed. Overall, these findings provide the first insights into the genetics of EC formation in “natural variants”, advancing our understanding of the molecular mechanisms regulating vascular variants in seed plants.

Premise of the study: Sabal minor is considered one of two cold tolerant palm species, inhabiting riparian zones in temperate and subtropical North America. Ecologically it is often overlooked due to its short compact underground stem that makes it appear stemless, or acaulescent. However, across the central US Gulf Coast S. minor is polymorphic for trunk type, with some individuals identified as caulescent, bearing an above-ground trunk that can reach up to two meters in height. Methods: We adopt a population genomics approach to characterize the genetic diversity of S. minor and to identify whether the caulescent and acaulescent forms of this temperate palm represent phenotypic variation within a single species. Key results: The caulescent and acaulescent forms are not reciprocally monophyletic, suggesting these two forms are phenotypic variants of a single species, S. minor s.l. Genetic clustering does not correspond to stem phenotype but rather reflects five discrete biogeographic clusters that span the native range. These geographic clusters indicate phylogeographic breaks along the Tombigbee River with a history that appears to be influenced by the delta of the Mississippi River. Two ecologically divergent populations, one in White Lake and another in Central Texas, show high genetic differentiation from surrounding populations indicating the presence of ecological barriers to gene flow. Conclusions: Population genetic structure of S. minor does not reflect stem morphotype (caulescence or acaulescence) supporting the current taxonomic recognition of one polymorphic species rather than two. However, populations of S. minor show genetic structuring corresponding to known phylogeographic barriers illustrating the dynamic roles regional landscape features played in shaping contemporary S. minor .

The taxonomic distinction between Arisaema japonicum and A. serratum has long been contentious, with treatments alternating between recognizing them as distinct species or conspecific variants. To resolve their taxonomic status, we conducted an integrative species delimitation analysis combining detailed morphological assessments with genome-wide single nucleotide polymorphism (SNP) data. Morphological investigations revealed continuous trait variation with numerous intermediates, precluding discrete morphological classification. Coalescent-based phylogenetic inference using Singular Value Decomposition Scores (SVDquartets) failed to recover A. japonicum as a monophyletic group, and principal component analysis of SNP data showed no genetic clustering corresponding to species boundaries. Species delimitation using Bayes Factor Delimitation (BFD) overwhelmingly supported a single-species model over competing hypotheses, including those based on previous morphological classifications. Together, these results indicate that A. japonicum does not represent a distinct evolutionary lineage and is best treated as conspecific with A. serratum. Our findings reconcile morphological and genetic data, providing strong support for the synonymization of A. japonicum under A. serratum, thereby resolving a longstanding taxonomic ambiguity within the genus Arisaema.

Target capture of ultraconserved elements (UCEs) and taxon-specific probes are widely used reduced-representation methods in phylogenomics and, increasingly, in population genomics for their ability to retrieve hundreds to thousands of homologous loci across divergent taxa. Meanwhile, declining costs and improved computational methods have made genome resequencing more accessible for non-model species, enabling the generation of datasets that can address evolutionary and ecological questions from micro- to macroevolutionary scales. Whether target capture approaches to likewise generate datasets that can address questions across broad hierarchical scales remains unclear. Here, we assess the efficacy of data collection (i.e., single nucleotide polymorphism (SNP) retention), predicted genetic variation across samples (i.e., heterozygosity), and phylogenetic congruence between data generated using reduced-representation methods and genome resequencing, leveraging publicly available datasets from plants and animals. We found that SNP retention varied by locus type, with genome-wide datasets retaining the highest proportion of SNPs and UCEs the lowest proportion. Heterozygosity also differed, with Benchmarking Universal Single-Copy Orthologs (BUSCOs) producing the lowest estimates, followed by UCEs; the inclusion of supercontig flanking regions raised heterozygosity values moderately. Across all phylogenetic trees, UCE datasets had the lowest bootstrap support, followed by BUSCOs and single copy orthologous genes. Population structure analyses frequently underestimated the number of ancestral populations in reduced-representation datasets, often identifying fewer populations than genome-wide datasets and assigning samples to different clusters. These discrepancies underscore the challenges of relying solely on reduced-representation methods for robust inferences of genetic diversity, phylogenetic relationships, and population structure.

The relationship between plants and their pollinators has played a crucial role in floral diversification throughout the evolution of angiosperms. The genus Costus L. presents floral morphologies associated with melittophilous and ornithophilous pollination syndromes, and species with intermediate morphology. To understand the origin of different morphologies within the genus, we used optical microscopy to analyse the floral ontogeny of seven Costus species with different floral morphologies. Our results demonstrate that the ontogeny of all species is similar in the early stages of development, and that disparity occurs later, mainly based on differences in growth of the staminodial labellum. Furthermore, we observed that in the early stages of development, the gynoecium of Costus presents bilateral symmetry, changing to an actinomorphic ovary and zygomorphic stigma at maturity. Thus, we suggest that the morphology of ornithophilous flowers arose from heterochronic events of the paedomorphy type. We also identified that this floral morphology, necessary for the transition between floral visitors, has evolved convergently through changes in the same developmental process. Our results also highlight similar patterns of gynoecium development and organization between Costaceae and Zingiberaceae, which may indicate a synapomorphy of these families.

Here we present a taxonomic revision of all neotropical Costaceae represented by 90 species, distributed in four monophyletic genera, Chamaecostus (9 spp.), Costus (76 spp.), Dimerocostus (5 spp.), and Monocostus (1 sp.). The work resulted in three new combinations, several nomenclatural changes, and four insufficiently known species are mentioned to demonstrate the need for continued and ongoing work on this charismatic yet often cryptic lineage of plants. We highlight the seventeen species of Costus and one species of Chamaecostus that were recently described (Maas et al. 2023) based on knowledge that emerged during this complete revisionary work, 60 years in the making. Included in this revision are details concerning the morphology, distribution, ecology, and phylogenetic relationships among the species studied. All currently recognized species are fully described, including notes on taxonomic synonymy, lectotypification, information on distribution and ecology, conservation status (either as evaluated and published in the IUCN Red List of Threatened Species or as estimated for this publication), vernacular names (when given) and short taxonomic notes. For each species, a distribution map is prepared and at least one colour photograph is included to assist in species identification. Dichotomous keys that include all species are provided, as is a list of all (c. 11.000) exsiccatae studied and an index to scientific names.