Biology subjects

Mandel, J. R.

Publications and source records attributed to Mandel, J. R..

7 recordsLinked to original sources

bioRxiv2026

The stability of fatty acid composition in sunflower oil is dependent on environment and affected by structural variation

In sunflower (Helianthus annuus L.), the composition of fatty acids in the seeds, primarily oleic, linoleic, stearic and palmitic acid, is of utmost importance for oil quality. Despite this, the genetic basis of this trait and its interaction with the environment is poorly understood. Understanding this interaction is critical to improvement of sunflower within the context of climate change. In this work, we incorporated fatty acid composition measurements from the sunflower SAM population and eight environments across an extensive geographic cline into GWAS. The SAM panel consists of 287 varieties representing approximately 90% of sunflower diversity, for which 2.2 million high-quality SNPs with a MAF > 5% are available. For increased power, multivariate GWAS was performed with four different inputs: (i) mean fatty acid composition within each environment, (ii) mean fatty acid composition within each environment omitting high oleic varieties, (iii) trait stability within environments quantified by standard errors among replicate samples ( stability) and (iv) Eberhart and Russells {beta} which quantifies trait stabilities across environments ({beta} stability). All four analyses yielded highly significantly associated SNPs. We found that high oleic varieties exhibited high {beta} trait stability, resulting in substantial overlap in markers between analyses (i) and (iv), with signals being fairly consistent between environments in analysis (i). For analyses (ii) and (iii), significant markers tended to vary between trials. For significant SNPs across all analyses, 147 candidate genes were identified, including promising candidates such as 15 fatty acid metabolism genes, 6 heat shock proteins and 22 transcription factors. Lastly, a large introgression consisting of two flanking inverted sequences on Chromosome 5 was found to coincide with stability in the Georgia trial, suggesting a role in FA composition stability under high heat conditions.

plant biology↗

bioRxiv2025

Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae

The flowering plant order Asterales exhibits a striking disparity in species richness, with >30,000 species in Asteraceae compared to <50 in its sister family Calyceraceae. To investigate the genomic basis of this imbalance, we assembled three new chromosome-level genomes, including the first for Calyceraceae, and re-annotated five additional genomes. Comparative analyses revealed exceptionally high repeat content in both Asteraceae and Calyceraceae, pervasive chromosomal rearrangements, and evidence for shared and lineage-specific WGDs. In Asteraceae, tandem and dispersed duplications disproportionately drove expansions of gene families linked to secondary metabolism and stress response, while segmental duplicates bore signatures of adaptive selection for the regulation of biosynthetic and metabolic processes. Selective pressures on flowering time regulators suggest an evolved balance between regulatory flexibility and developmental constraint in floral diversification. These patterns reveal that, beyond ancient polyploidy, small-scale duplications and selective fine-tuning of regulatory networks underpinned the ecological versatility in Asteraceae, fueling its extraordinary diversification.

genomics↗

bioRxiv2025

Floral innovation through modifications in stem cell peptide signaling.

Understanding how evolution shapes genetic networks to create new developmental forms is a central question in biology. Asteraceae (sunflower family) comprise 10% of flowering plants and have capitula, a novel flowering shoot (inflorescence) that mimics a single flower (1, 2). During capitulum development, shoot stem cells undergo prolonged proliferation relative to other species (3, 4). Here we show that capitulum evolution paralleled decreases in CLAVATA3 peptide (CLV3p) signaling, a conserved repressor of stem cell proliferation. Asteraceae CLV3p displays reduced receptor binding and downstream transcriptional outputs. Reversion of CLV3 to a more active form impairs Asteraceae stem cell regulation and capitulum development. Lastly, we trace CLV3 evolution across the Asterales allowing inferences on capitulum evolution. Our findings reveal novel evolutionary mechanisms in plant reproduction and suggest approaches for engineering crops.

plant biology↗

bioRxiv2023

From paralogy to hybridization: Investigating causes of underlying phylogenomic discordance using the complex genus Packera (Senecioneae; Asteraceae)

Premise of the studyUnderlying discordance in phylogenomic studies is becoming more common, and the answer is not as simple as adding more data. Biological processes such as polyploidy, hybridization, and incomplete lineage sorting are main contributors to these issues and must be considered when generating phylogenies. Otherwise, interpretations of evolutionary relationships could be misleading. MethodsTo obtain a better understanding of potential gene flow and its effect on phylogenetic trees, we investigated the causes and consequences of nuclear discordance using the genus Packera to understand how they influence the phylogenetic patterns seen in this complex group. To do this, we compared the topology and support values of Packera phylogenies resulting from various paralog selection or pruning methods. We then investigated whether pruning the paralogs instead of performing a selection process affected the topology and support of our phylogeny. To investigate hybridization and its effect on species relationships in our tree, we used likelihood methods to infer phylogenetic networks to find any evidence of gene flow among species lineages in this complicated genus. Key resultsWe found that performing different paralog selection or pruning methods does impact our understanding of the evolutionary relationships within Packera, and that addressing these paralogs with more rigorous methods than the typical pipeline increases concordance within the resulting phylogenies. Additionally, investigating reticulation events within highly discordant clades showed that ancestral hybridization and reticulation events are common throughout Packera. ConclusionsInvestigating underlying biological processes by testing various methods can provide further insight into complex species relationships and levels of discordance within phylogenomic studies.

evolutionary biology↗

bioRxiv2023

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

PremiseThe sunflower family specific probe set, Compositae-1061, has enabled family-wide phylogenomic studies and investigations at lower-taxonomic levels by targeting 1,000+ genes. However, it generally lacks resolution at the genus to species level, especially in groups with complex evolutionary histories including polyploidy and hybridization. MethodsIn this study, we developed a new Hyb-Seq probe set, Compositae-ParaLoss-1272, designed to target orthologous loci in Asteraceae family members. We tested its efficiency across the family by simulating target-enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in genus Packera which has a complex evolutionary and taxonomic history. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 taxa which were previously studied using the Compositae-1061 probe set. Sequences from both probe sets were used to generate phylogenies, compare topologies, and assess node support. ResultsWe report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members. Additionally, Compositae-ParaLoss-1272 had less gene tree discordance, recovered considerably fewer paralogous sequences, and retained longer loci than Compositae-1061. DiscussionGiven the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate this new probe set will provide improved resolution and utility for studies at lower-taxonomic levels and complex groups in the sunflower family.

plant biology↗

bioRxiv2023

Resolving evolutionary relationships in the groundsels: phylogenomics, divergence time estimates, and biogeography of Packera (Asteraceae: Senecioneae)

The genus Packera belongs to the sunflower family and contains an estimated 64 species and varieties endemic to North America. Some Packera are known to hybridize or exhibit polyploidy, making it difficult to reconstruct evolutionary relationships within the group. Previous molecular phylogenetic studies of Packera employing ITS data recovered low resolution trees, providing little information on the evolutionary relationships within this complex genus. Therefore, we used next-generation sequencing data to infer nuclear and plastid phylogenies of Packera and related Senecioneae taxa. The nuclear phylogeny was calibrated to produce a timetree, then used to reconstruct the macroevolutionary history of Packera, including its historical biogeography. We then compared the reconstructed evolutionary history to previously published scenarios based on phylogenetic and geohistorical data. We found that the nuclear and plastid phylogenies were highly incongruent, with the nuclear tree presenting higher resolution than the plastid tree which had an apparent lack of plastid diversity. The nuclear tree indicated that geography may have played a major role in the evolution and taxonomic diversification of Packera. The estimated origin of Packera at approximately 19.2MY - 25.9MY (late Oligocene to early Miocene) is older than in most other studies. Nonetheless, it aligns well with previous geohistorical predictions, which suggest that speciation and diversification events in Packera were driven by changes in geography and climate in North America. Moreover, Packera likely originated in the western United States or Mexico, and subsequently diversified north and east into the rest of North America and Russia, in agreement with other studies.

plant biology↗

bioRxiv2021

Rapid evolution of weedy traits during sunflower de-domestication: the importance of hybridization and standing genetic variation

Hybridization between crops and their wild relatives may promote the evolution of de-domesticated (feral) weeds. Wild sunflower (Helianthus annuus L.) is typically found in ruderal environments, but crop-wild hybridization may facilitate the evolution of weedy populations. Using one crop-specific mitochondrial marker (CMS-PET1) and 14 nuclear SSR markers, we studied the origin and genetic diversity of a recently discovered weedy population of sunflower (named BRW). Then, using a resurrection approach, we tested for rapid evolution of weedy traits (seed dormancy, herbicide resistance, and competitive ability) by sampling weedy and wild populations 10 years apart (2007 and 2017). All the weedy plants present the CMS-PET1 cytotype, confirming their feral origin. At the nuclear markers, BRW showed higher genetic diversity than the cultivated lines and low differentiation with one wild population, suggesting that wild hybridization increased their genetic diversity. We found support for rapid evolution towards higher seed dormancy, but not for higher competitive ability or herbicide resistance. Our results highlight the importance of seed dormancy during the earliest stages of adaptation and show that crop-wild hybrids can evolve quickly in agricultural environments.

plant biology↗