Biology subjects

Deanna, R.

Publications and source records attributed to Deanna, R..

9 recordsLinked to original sources

bioRxiv2026

Reticulate History of Southern South American Wild Potatoes: Recurrent Hybridization, Cytonuclear Discordance, and Phylogenetic Placement of Solanum malmeanum

Hybridization is a powerful process in plant evolution generating reticulate patterns of speciation, introgression, and chloroplast capture. In the Petota clade of Solanum, which spans cultivated and wild potatoes, these processes cause much of the taxonomic complexity of the group. We examined the evolutionary history of the Commersoniana group (Solanum commersonii and S. malmeanum) relative to S. chacoense (Tuberosa Group) using an integrative framework of phylogenomics and morphology. With target-capture sequencing (Angiosperms353) of nuclear and plastid loci recovered from herbarium specimens, together with data mining we built nuclear and plastome phylogenies and ran symmetry tests, gene concordance analyses, and coalescent simulations to weigh incomplete lineage sorting against chloroplast capture. The data reveal cytonuclear discordance and events consistent with chloroplast capture from S. chacoense into Commersoniana lineages supported by both empirical and simulated results. Phylogenetic networks confirm repeated historical and recent reticulation, especially involving S. malmeanum. Non-metric Multidimensional Scaling (NMDS) of morphological traits did not recover clear species boundaries but was consistent with a hybrid origin for the group. These results indicate that recurrent hybridization and event consistent with chloroplast capture are strongly influencing evolution in the examined wild potatoes, complicating classical taxonomy and informing conservation and breeding. They also underscore the value of combining genomic and phenotypic data to resolve species boundaries in plant groups with tangled hybrid histories.

evolutionary biology↗

bioRxiv2026

Catcher in the rye: museomics reveals the identity of cereal remains recovered from a late nineteenth century antique furniture

Historical crop remains preserved in everyday objects are an underused archive of agrobiodiversity change, yet their degraded DNA resists conventional analysis. We recovered cereal grains and straws used as upholstery padding in a Central European settee dated to about 1870 to 1900. We identified and characterized the specimen by genome skimming. Damage-aware sequencing confirmed authentic historical DNA of modest, late nineteenth-century age. The assembled plastome placed the specimen securely within rye, and a genome-wide SNP panel of rye landraces resolved it inside cultivated Secale cereale subsp. cereale, closest to a Hungarian bred rye and a Slovak upland landrace and remote from wild or eastern lineages. Screening 192 stress-associated loci recovered the structural machinery of resistance, abiotic stress and aluminum tolerance pathways, while heading-date genotyping showed the Weining earliness allele at Hd2R already present. Divergence across 36 domestication sweep regions concentrated at a few improvement loci. Integrating these genomic signals with genebank passport data and an 1891 newspaper record, we interpret the specimen as a tall Central European rye at the threshold between landrace and improved variety. Historical crop material, read this way, preserves both genomes and the traces of human agricultural practice.

genomics↗

bioRxiv2025

Late Cretaceous origins for major nightshade lineages from total evidence timetree analysis

Background and AimsThe timing of the radiation of nightshades (Solanaceae) has been contentious in the literature, with estimates of the crown age ranging from ca. 30 to 70 Mya (mid-Oligocene to late Cretaceous). The tempo of diversification of major lineages within the family (e.g., berries, tobaccos) has been equally challenging to resolve, in large part because of the paucity of fossil information. Recently described fossils present an opportunity to revisit the timing of nightshade diversification using more powerful model-based methods. Here, we simultaneously infer divergence times within Solanaceae and the placement of a select set of well-preserved and morphologically diverse fruit and seed fossils. MethodsWe assembled a family-wide morphological dataset, including 17 categorical and eight continuous characters, for 134 living and 14 fossil Solanaceae taxa, as well as sequence data for the extant taxa. We implemented a Bayesian total evidence dating analysis in RevBayes using (a time continuous and a time heterogeneous) fossilized birth-death model and models of character evolution for each type of data. Key ResultsThe origin of Solanaceae was [~]98 Mya, and the major splits were roughly three-fold older than previously estimated. Although the 14 fossil taxa were phylogenetically placed with different degrees of confidence, we identified a fruit fossil and a seed fossil whose affinities were strongly supported. Moreover, most of the fossils lacking a precise placement were nevertheless confidently inferred to belong to the large berry clade. ConclusionsOur study provides an example of how a sophisticated model used on a carefully assembled dataset can shed light on the timing of the evolution of a group, while accounting for phylogenetic uncertainty. The timetree we present here provides a temporal framework for further research, from comparative genomics and patterns of diversification to trait evolution and biogeography.

evolutionary biology↗

bioRxiv2025

Novel production of structurally diverse and sticky defense metabolites on wild tomatillo fruits

Plants have evolved a structurally diverse chemical repertoire to mediate various environmental interactions. Yet, little is known about the chemical complexity and metabolic pathways across many plant genera. Acylsugars are a class of specialized metabolites widely distributed across the Solanaceae that play a role in defense. Although acylsugars have been extensively characterized from leaf glandular trichomes, they have also been detected in other tissues. Nevertheless, acylsugar structures, biosynthesis, and functions outside of leaf trichomes remain unknown. Here, we performed tissue specific metabolomics across 29 Physalis species, an emerging model and crop genus closely related to important Solanum crops. Automated mass spec feature identification and library searches from surface extracts of leaf, calyx, and fruit tissues revealed metabolite diversity including putative metabolite classes of flavonoids, phenolics, and terpenoids. Acylsugar mass spec features were manually annotated, revealing at least 323 unique acylsugars - substantially expanding the known Physalis acylsugar diversity. Some, but not all, Physalis species accumulated acylsugars on the trichome-less fruit surface, and were as abundant or sometimes more abundant, in fruits than in leaves or calyces. Hierarchical clustering and phylogenetic tests indicated that species with similar acylsugar profiles do not cluster taxonomically. To determine the biochemical mechanism underlying acylsugar structural diversity, we characterized the first step of acylsugar biosynthesis, catalyzed by an acylsugar acyltransferase (ASAT). ASAT1s from three Physalis species displayed broad substrate preferences, which may explain the differences in acylsugar profiles. The diverse fruit-localized acylsugars across Physalis can inform engineering strategies for increased crop resilience.

plant biology↗

bioRxiv2025

A new phylogeny and phylogenetic classification for Solanaceae

Solanaceae are a globally distributed family of considerable economic importance. Recent phylogenetic work on various clades in the family has resulted in a plethora of names at various taxonomic levels. This results in a confusing set of names applied to clades at different ranks, and to the use of informal names that are often not accepted in online resources. To solve this problem, we present here a phylogenetic classification following the PhyloCode for the Solanaceae. Traditional taxon names previously recognized at the ranks of tribe, genus, and section were maintained when associated with clades. We base our clade definitions on a newly constructed phylogeny of the family using 10 plastid and nuclear markers with a broad sampling of 1,474 species, roughly half of the diversity of the family. We complement this marker-based analysis with a phylogenomic analysis of 110 taxa (including 97 of the 102 genera in the family) using the Angiosperms353 probe set. This pair of analyses produced highly concordant phylogenies and provides strong support for the clades included in the classification. In total, we propose and define rank-free names for 38 major clades, including 16 infrageneric taxa within the mega-diverse Solanum. This rank-free system intends to promote name stability as new data become available, avoiding name changes to well-known groups.

evolutionary biology↗

bioRxiv2025

Seed fossil record of Solanaceae revisited

The fossil record for Solanaceae has a complex taxonomic history, with many species originally described in the family being subsequently shown to belong in other plant families. In this work, we present an in-depth analysis of the nightshade seed fossil record, which corresponds to the largest amount of fossil material for the family despite having relatively few described taxa. We re-examined 110 fossil seeds previously assigned either to one of the six taxa or unplaced within the family. All fossils were imaged and measured for 14 discrete and continuous characters, and a subset of 22 well-preserved specimens was additionally subjected to micro-CT scanning. In parallel, we scored the same set of characters for seeds from 354 extant taxa of Solanaceae. We carried out a multivariate analysis of the combined extinct and extant dataset to visualize the placement of fossil seeds within Solanaceae seed morphospace. This analysis revealed a wide spread of fossils across morphospace, including a variety of shapes, sizes and testal wall features. For one fossil taxon (Hyoscyosperma daturoides Deanna & S.D.Sm. gen. et sp. nov.), the micro-CT images confirmed the presence of an elaiosome, otherwise only known in the family from the genus Datura L. Based on these analyses, we re-circumscribe three species and describe six new taxa (four in new genera), doubling the number of fossil seed species in the family. The broad geographic and stratigraphic distribution of these diverse taxa, from Eocene North America and Europe to Pleistocene Eurasia, support the notion that the Solanaceae is likely a family of a late Cretaceous origin that attained nearly a cosmopolitan distribution by the Eocene.

paleontology↗

bioRxiv2020

Building a pathway for diversity in plant sciences in Argentina: highlighting the work of women scientists through virtual activities

Encouraging the participation of a diverse workforce in academia increases plurality as it broadens the range of skills, ways of thinking and experiences. Institutions and professional societies have been putting efforts on building plans that help make workplaces, conferences, education and extension programs more relatable to a highly diverse population. Argentina has an overall gender-balanced workforce in the sciences (~53% women/total), with an even higher representation in disciplines related to plant sciences. However, media outlets and national conferences related to genetics, botany, plant physiology, ecology and molecular biology, fail to reflect those numbers as the proportion of women invited for interviews, plenary lectures, and symposia falls below ~30%. As a way to increase the visibility of the wealth of plant science topics and experimental approaches in which Argentinian women work, and to facilitate connections among them across the country and abroad, we created the Argentinian Women in Plant Science network (https://argplantwomen.weebly.com/). This group has grown to over 200 members, representing a wide range of career stages and research topics. Since April, and taking advantage of the confinement situation, our weekly webinar series highlighting women plant scientists has reached an average audience of 60-70 participants, with a record of 100. Recently, we have begun a series of open professional development webinars to reach a wider public. Our first webinar, focused on Scientific poster design, had ~250 participants, most of them undergrad and graduate students from all over the country covering a diverse range of disciplines, including the social sciences. Even though we have immersed ourselves in the plant science community with our weekly seminars, we have expanded our goals with activities aimed to reach out to a much wider audience with webinars and teacher training workshops, hopefully making plant science more attainable to all.

scientific communication and education↗

bioRxiv2020

Karyotype asymmetry shapes diversity within the physaloids (Physalidinae, Physalideae, Solanaceae)

Within the cosmopolitan family Solanaceae, Physalideae is the tribe with the highest generic diversity (30 genera and more than 200 species). This tribe embraces subtribe Physalidinae, in which positions of some genera are not entirely resolved. Chromosomes may help on this goal, by providing information on the processes underlying speciation. Thus, cytogenetic analyses were carried out in the subtribe in order to establish its chromosome number and morphology. Physalidinae is characterized by x = 12 and most species shows a highly asymmetric karyotype. These karyotype traits were mapped onto a molecular phylogeny to test the congruence between karyotype evolution and clade differentiation. A diploid ancestor was reconstructed for the subtribe, and five to six polyploidy independent events were estimated, plus one aneuploidy event (X = 11 in the monotypic genus Quincula). Comparative phylogenetic methods showed that asymmetry indices and chromosome arm ratio (r) have a high phylogenetic signal, whereas the number of telocentric and submetacentric chromosomes presented a conspicuous amount of changes. Karyotype asymmetry allow us to differentiate genera within the subtribe. Overall, our study suggests that Physalidineae diversification has been accompanied by karyotype changes, which can be applied to delimit genera within the group.

plant biology↗

bioRxiv2018

Repeated evolution of a morphological novelty: a phylogenetic analysis of the inflated fruiting calyx in the Physalideae tribe (Solanaceae)

PREMISE OF THE STUDYThe evolution of novel fruit morphologies has been integral to the success of angiosperms. The inflated fruiting calyx, in which the balloon-like calyx swells to completely surround the fruit, has evolved repeatedly across angiosperms and is postulated to aid in protection and dispersal. Here we investigate the evolution of this trait in the tomatillos and their allies (Physalideae, Solanaceae), using a newly estimated phylogeny and a suite of comparative methods to infer evolutionary gains and losses.\n\nMETHODSThe Physalideae phylogeny was estimated using DNA sequences from four regions (ITS, LEAFY, trnL-F, waxy) using maximum likelihood and Bayesian Inference. Maximum likelihood model selection was used to determine the best fitting model of trait evolution. Using this model, we estimated ancestral states along with the numbers of gains and losses of fruiting calyx accrescence and inflation with Bayesian stochastic mapping. Also, phylogenetic signal in calyx morphology was examined with two metrics (parsimony score and Fritz and Purvis D).\n\nKEY RESULTSThe well resolved phylogeny points to multiple taxa in need of revision, including the eight genera that are non-monophyletic as presently circumscribed. Model fitting indicated that calyx evolution has proceeded in stepwise fashion, from non-accrescent, to accrescent, to inflated. Moreover, these transitions appear to be largely irreversible. Among the 215 sampled Physalideae, we inferred 24 gains of fruiting calyx accrescence, 24 subsequent transitions to a fully inflated calyx and only two reversals. A median of 50 shifts were estimated in total across the clade from the ancestral non-accrescent calyx. Nonetheless, fruiting calyx accrescence and inflation show strong phylogenetic signal.\n\nCONCLUSIONSOur phylogeny greatly improves the resolution of Physalideae and highlights the need for taxonomic work. The analyses of trait evolution reveal that the inflated fruiting calyx has evolved many times and that the trajectory towards this phenotype is generally stepwise and directional. These results provide a strong foundation for studying the genetic and developmental mechanisms responsible for the repeated origins of this charismatic fruit trait.

evolutionary biology↗