Biology subjects

Sapir, Y.

Publications and source records attributed to Sapir, Y..

8 recordsLinked to original sources

bioRxiv2025

Evolutionary history, ecological divergence, and introgression in the Oncocyclus irises species complex in the Southern Levant

Speciation is a dynamic process shaped by the interaction of gene flow, geographic isolation, and ecological divergence. The Oncocyclus irises of the Southern Levant represent a young radiation of narrowly endemic species considered to be in the course of speciation. In this study, we used RAD-sequencing and single nucleotide polymorphism analysis across nine described species to investigate patterns of genomic divergence, gene flow, and local adaptation. Phylogenomic analyses revealed a mix of well-supported clades for some species, previously defined by their morphology and distribution, and non-monophyletic lineages, with several species exhibiting shallow divergence and shared genetic ancestry. We found evidence for gene flow and historical introgression between Iris petrana, I. atrofusca and I. mariae, while other cases of non-monophyly appear driven by incomplete lineage sorting. Both geographic distance (IBD) and environmental factors (IBE), mainly altitude, temperature, and aridity, were significantly associated with genetic structure, suggesting that local adaptation contributed to divergence following range expansion. Based on our findings we propose that the divergence of the Oncocyclus iris species in the Southern Levant supports a stepping-stone dispersion model, in which north-to-south dispersal was followed by local adaptation, and introgression in secondary contact zones. Overall, these findings highlight the complexity of speciation and the need for integrative approaches to study the interplay between historical divergence, contemporary gene flow, and environmental differentiation in shaping genomic patterns.

evolutionary biology↗

bioRxiv2021

A Cultured Sensorimotor Organoid Model Forms Human Neuromuscular Junctions

Human induced pluripotent stem cells (iPSCs) hold promise for modeling diseases in individual human genetic backgrounds and thus for developing precision medicine. Here, we generate sensorimotor organoids containing physiologically functional neuromuscular junctions (NMJs) within a cultured organoid system and apply the model to different subgroups of amyotrophic lateral sclerosis (ALS). Using a range of molecular, genomic, and physiological techniques, we identify and characterize motor neurons and skeletal muscle, along with sensory neurons, astrocytes, microglia, and vasculature. Organoid cultures derived from ALS subject iPSC lines and isogenic lines edited to harbor familial ALS mutations all show impairment at the level of the NMJ, as detected by both contraction and immunocytochemical measurements. The physiological resolution of the human NMJ synapse, combined with the generation of major cellular cohorts exerting autonomous and non-cell autonomous effects in motor and sensory diseases, may prove valuable for more comprehensive disease modeling.

neuroscience↗

bioRxiv2021

A high-content platform for physiological profiling and unbiased classification of individual neurons

High-throughput physiological assays often lose single cell resolution, precluding subtype-specific analyses of neuronal activation mechanism and drug effects. Here, we demonstrate APPOINT, Automated Physiological Phenotyping Of Individual Neuronal Types. This physiological assay platform combines calcium imaging, robotic liquid handling, and automated analysis to generate physiological activation profiles of single neurons at a large scale. Using unbiased techniques, we quantify responses to multiple sequential stimuli, enabling subgroup identification by physiology and probing of distinct mechanisms of neuronal activation within subgroups. Using APPOINT, we quantify primary sensory neuron activation by metabotropic receptor agonists and identify potential contributors to pain signaling. Furthermore, we expand the role of neuroimmune interactions by showing that human serum can directly activate sensory neurons, elucidating a new potential pain mechanism. Finally, we apply APPOINT to develop a high-throughput, all-optical approach for quantification of activation threshold and pharmacologically separate the contributions of distinct ion channel subsets to optical activation.

neuroscience↗

bioRxiv2019

Local adaptation to abiotic and biotic stresses and phenotypic selection on flowering time in annual Brachypodium spp. along an aridity gradient

O_LIPlants have diverse strategies to cope with stress, including early flowering to \"escape\" abiotic stress and late flowering to mitigate biotic stress. Plants are usually exposed to multiple stresses simultaneously, but little is known about the impact of multiple co-occurring stresses on plant evolution.\nC_LIO_LIWe tested for adaptation to both aridity and interspecific competition of the model plant Brachypodium spp., collected along the aridity gradient in Israel. We recorded flowering time and estimated fitness in a controlled watering experiment, with treatments mimicking Mediterranean and arid precipitation, and in two common gardens located in the extremes of the gradient (i.e., desert and mesic Mediterranean). At the latter we also manipulated interspecific competition to examine the combined effect of competition and aridity.\nC_LIO_LIPlants from arid environments always flowered earlier, but we found no selection on flowering time in the watering experiment. In the common gardens, however, the direction of selection on flowering time differed between sites and competition treatments.\nC_LIO_LIWe conclude that interactions between aridity and competition drive local adaptation of Brachypodium in the Eastern Mediterranean basin. Variation in flowering time is an important adaptive mechanism to aridity and multiple selection agents can have interactive effects on the evolution of this trait.\nC_LI

evolutionary biology↗

bioRxiv2019

De novo Transcriptome Characterization of Royal Iris (Iris section Oncocyclus) and Identification of Flower Development Genes

The Royal Irises, Iris section Oncocyclus, are a Middle-Eastern group of irises, characterized by extremely large flowers with a huge range of flower colors and a unique pollination system. The Royal Irises are considered to be in the course of speciation and serve as a model for evolutionary processes of speciation and pollination ecology. However, no transcriptomic and genomic data for molecular characterization are available for these plants. Transcriptome sequencing is a valuable resource for determining the genetic basis of ecological-meaningful traits, especially in non-model organisms. Here we describe the de novo transcriptome sequencing and assembly of Iris atropurpurea, an endangered species, endemic to Israels coastal plain. We employed RNA sequencing to analyze the transcriptomes of roots, leaves, and three stages of developing flower buds. To identify genes involved in developmental processes we generated phylogenetic gene trees for two major gene families, the MADS-box and MYB transcription factors, which play an important role in plant development. In addition, we identified 1,503 short sequence repeats that can be developed for molecular markers for population genetics in irises. In the era of large genetic datasets, the Iris transcriptome sequencing provides a valuable resource for studying adaptation-associated traits in this non-model plant. This first reported transcriptome for the Royal Irises, and the data generated from this study, will facilitate gene discovery, functional genomic studies, and development of molecular markers in irises, to complete the intensive eco-evolutionary studies of this group.

plant biology↗

bioRxiv2018

Flowers respond to pollinator sound within minutes by increasing nectar sugar concentration.

Can plants hear? That is, can they sense airborne sounds and respond to them? Here we show that Oenothera drummondii flowers, exposed to the playback sound of a flying bee or to synthetic sound-signals at similar frequencies, produced sweeter nectar within 3 minutes, potentially increasing the chances of cross pollination. We found that the flowers vibrated mechanically in response to these sounds, suggesting a plausible mechanism where the flower serves as the plants auditory sensory organ. Both the vibration and the nectar response were frequency-specific: the flowers responded to pollinator sounds, but not to higher frequency sound. Our results document for the first time that plants can rapidly respond to pollinator sounds in an ecologically relevant way. Sensitivity of plants to pollinator sound can affect plant-pollinator interactions in a wide range of ways: Plants could allocate their resources more adequately, focusing on the time of pollinator activity; pollinators would then be better rewarded per time unit; flower shape may be selected for its effect on hearing ability, and not only on signaling; and pollinators may evolve to make sounds that the flowers can hear. Finally, our results suggest that plants may be affected by other sounds as well, including antropogenic ones.

ecology↗

bioRxiv2017

Does floral herbivory reduce pollination-mediated fitness in shelter rewarding Royal Irises?

Florivory, the damage to flowers by herbivores can affect fitness both directly and indirectly. Flowers consumed by florivores may fail to produce fruit or produce lower seed set because of direct damage to reproductive organs. In addition, eaten flowers are less attractive to pollinators because of reduced or modified advertisement, which reduces pollination services. While observational data are abundant, experimental evidence is scarce and results are contrasting. We tested experimentally the effect of florivory on both pollinator visitation and reproductive success in three species of the Royal Irises, which have large flowers that are attractive to pollinators, and potentially also for florivores. We hypothesized that florivory will reduce pollen deposition due to reduced attractiveness to pollinators, while fruit set and seed set will depend on the extent of florivory. We performed artificial florivory in two experiments over two years. In the first experiment, each of the three floral units of a single Iris flower was subject to either low or high artificial florivory, or left un-touched as control. We counted the number of pollen grains deposited on each of the three stigmas as a measure of pollinator visitation. In the second experiment, three flowers of the same plant received low, high, or no artificial florivory and were further recorded for fruit and seed production. In 2016, high artificial florivory revealed lower number of pollen grains on stigmas of Iris atropurpurea, but in 2017 there was no difference. Similarly, number of pollen grains in high artificial was lower than low florivory in 2017 in I. petrana. No significant effect of florivory was found on pollen grain deposition, fruit set or seed set. The results remained consistent across species and across years. The results undermine the assumption that flower herbivory is necessarily antagonistic interaction and suggests that florivores may not be strong selection agents on floral reproductive biology in the Oncocyclus irises.

ecology↗

bioRxiv2017

Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly

X-linked Dystonia-Parkinsonism (XDP) is a Mendelian neurodegenerative disease endemic to the Philippines. We integrated genome and transcriptome assembly with induced pluripotent stem cell-based modeling to identify the XDP causal locus and potential pathogenic mechanism. Genome sequencing identified novel variation that was shared by all probands and three recombination events that narrowed the causal locus to a genomic segment including TAF1. Transcriptome assembly in neural derivative cells discovered novel TAF1 transcripts, including a truncated transcript exclusively observed in probands that involved aberrant splicing and intron retention (IR) associated with a SINE-VNTR-Alu (SVA)-type retrotransposon insertion. This IR correlated with decreased expression of the predominant TAF1 transcript and altered expression of neurodevelopmental genes; both the IR and aberrant TAF1 expression patterns were rescued by CRISPR/Cas9 excision of the SVA. These data suggest a unique genomic cause of XDP and may provide a roadmap for integrative genomic studies in other unsolved Mendelian disorders.\n\nHighlights O_LIGenome assembly narrows the XDP causal locus to a segment including TAF1\nC_LIO_LIXDP-specific SVA insertion induces intron retention and down-regulation of TAF1\nC_LIO_LICRISPR/Cas9 excision of SVA rescues aberrant splicing and cTAF1 expression in XDP\nC_LIO_LIGene networks perturbed in proband cells associate to synapse and neurodevelopment\nC_LI

genomics↗