Biology subjects

Levine, J.

Publications and source records attributed to Levine, J..

5 recordsLinked to original sources

bioRxiv2018

Ecosystem tipping points in an evolving world

There is growing concern over tipping points arising in ecosystems due to the crossing of environmental thresholds. Tipping points lead to strong and possibly irreversible shifts between alternative ecosystem states incurring high societal costs. Traits are central to the feedbacks that maintain alternative ecosystem states, as they govern the responses of populations to environmental change that could stabilize or destabilize ecosystem states. However, we know little about how evolutionary changes in trait distributions over time affect the occurrence of tipping points, and even less about how big scale ecological shifts reciprocally interact with trait dynamics. We argue that interactions between ecological and evolutionary processes should be taken into account for understanding the balance of feedbacks governing tipping points in nature.

ecology↗

bioRxiv2018

Chemical signatures of honey bee group membership develop via a socially-modulated innate process

Large social insect colonies exhibit a remarkable ability for recognizing group members via colony-specific cuticular hydrocarbon (CHC) pheromonal signatures. Previous work suggested that in some ant species colony-specific signatures are generated through a \"gestalt\" mechanism via the passive transfer and homogenization of CHCs across all individual members of the colony. In contrast, we demonstrate that nestmate recognition cues of worker honey bees (Apis mellifera) mature in foragers via a sequence of stereotypic age-dependent quantitative and qualitative chemical transitions, which are driven by intrinsic biosynthetic pathways. Therefore, in contrast to predictions of the \"Gestalt\" model, nestmate recognition cues in honey bee colonies do not represent a passive \"average\" signature that is carried and recognized by all colony members. Instead, specific colony members develop the relevant cues via an innately-determined developmental program that can be modulated by colony-specific social environmental factors.

animal behavior and cognition↗

bioRxiv2018

Palantir characterizes cell fate continuities in human hematopoiesis

Recent studies using single cell RNA-seq (scRNA-seq) data derived from differentiating systems have raised fundamental questions regarding the discrete vs continuous nature of both differentiation and cell fate. Here we present Palantir, an algorithm that models trajectories of differentiating cells, which treats cell-fate as a probabilistic process, and leverages entropy to measure the changing nature of cell plasticity along the differentiation trajectory. Palantir generates a high resolution pseudotime ordering of cells, and assigns each cell state with its probability to differentiate into each terminal state. We apply Palantir to human bone marrow scRNA-seq data and detect key landmarks of hematopoietic differentiation. Palantirs resolution enables identification of key transcription factors driving lineage fate choices, as these TFs closely track when cells lose plasticity. We demonstrate that Palantir is generalizable to diverse tissue types and well-suited to resolve less studied differentiating systems.

systems biology↗

bioRxiv2018

Tissue-specific cis-regulatory divergence implicates a fatty acid elongase necessary for inhibiting interspecies mating in Drosophila

Pheromones known as cuticular hydrocarbons are a major component of reproductive isolation in Drosophila. Individuals from morphologically similar sister species produce different sets of hydrocarbons that allow potential mates to identify them as a suitable partner. In order to explore the molecular mechanisms underlying speciation, we performed RNA-seq in F1 hybrids to measure tissue-specific cis-regulatory divergence between the sister species D. simulans and D. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. We found that one of these, the fatty acid elongase eloF, broadly affects both the complement of hydrocarbons present on D. sechellia females and the propensity of D. simulans males to mate with those females. In addition, knockdown of eloF in the more distantly related D. melanogaster led to a similar shift in hydrocarbons as well as lower interspecific mate discrimination by D. simulans males. Thus, cis-regulatory changes in eloF appear to be a major driver in the sexual isolation of D. simulans from multiple other species. More generally, our RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes; the same framework can be used to pinpoint cis-regulatory drivers of divergence in a wide range of traits differing between any interfertile species.

systems biology↗

bioRxiv2018

Can Drosophila melanogaster tell who’s who?

Drosophila melanogaster are known to live in a social but cryptic world of touch and odours, but the extent to which they can perceive and integrate visual information is a hotly debated topic. Some researchers fixate on the limited resolution of D. melanogasters optics, others on their seemingly identical appearance; yet there is evidence of individual recognition and surprising visual learning in flies. Here, we apply machine learning and show that individual D. melanogaster are visually distinct. We also use the striking similarity of Drosophilas visual system to current convolutional neural networks to theoretically investigate D. melanogasters capacity for visual understanding. We find that, despite their limited optical resolution, D. melanogasters neuronal architecture has the capability to extract and encode a rich feature set that allows flies to re-identify individual conspecifics with surprising accuracy. These experiments provide a proof of principle that Drosophila inhabit in a much more complex visual world than previously appreciated.\n\nAuthor summaryIn this paper, we determine a proof of principle for inter-individual recognition in two parts; is there enough information contained in low resolution pictures for inter-fly discrimination, and if so does Drosophilas visual system have enough capacity to use it. We show that the information contained in a 29x29 pixel image (number of ommatidia in a fly eye) is sufficient to achieve 94% accuracy in fly re-identification. Further, we show that the fly eye has the theoretical capacity to identify another fly with about 75% accuracy. Although it is unlikely that flies use the exact algorithm we tested, our results show that, in principle, flies may be using visual perception in ways that are not usually appreciated.

animal behavior and cognition↗