Climate-induced phenological shifts in a Batesian mimicry complex

Climate-induced changes in spatial and temporal occurrence of species, as well as species traits such as body size, each have the potential to decouple symbiotic relationships. Past work has focused primarily on direct interactions, particularly those between predators and prey and between plants and pollinators, but studies have rarely demonstrated significant fitness costs to the interacting, coevolving organisms. Here, we demonstrate that changing phenological synchrony in the latter part of the 20th century has different fitness outcomes for the actors within a Batesian mimicry complex, where predators learn to differentiate harmful “model” organisms (stinging Hymenoptera) from harmless “mimics” (hoverflies, Diptera: Syrphidae). We define the mimetic relationships between 2,352 pairs of stinging Hymenoptera and their Syrphidae mimics based on a large-scale citizen science project and demonstrate that there is no relationship between the phenological shifts of models and their mimics. Using computer game-based experiments, we confirm that the fitness of models, mimics, and predators differs among phenological scenarios, creating a phenologically antagonistic system. Finally, we show that climate change is increasing the proportion of mimetic interactions in which models occur first and reducing mimic-first and random patterns of occurrence, potentially leading to complex fitness costs and benefits across all three actors. Our results provide strong evidence for an overlooked example of fitness consequences from changing phenological synchrony.

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A trait-based approach to assess climate change sensitivity of freshwater invertebrates across Swedish ecoregions

Current Zoology ◽

10.1093/czoolo/60.2.221 ◽

2014 ◽

Vol 60 (2) ◽

pp. 221-232 ◽

Cited By ~ 11

Author(s):

Leonard Sandin ◽

Astrid Schmidt-Kloiber ◽

Jens-Christian Svenning ◽

Erik Jeppesen ◽

Nikolai Friberg

Keyword(s):

Climate Change ◽

Global Climate Change ◽

Large Scale ◽

Global Climate ◽

Species Traits ◽

Freshwater Ecosystems ◽

Biological Data ◽

Conservation Strategies ◽

Measured Temperature ◽

Buffer Strips

Abstract Freshwater habitats and organisms are among the most threatened on Earth, and freshwater ecosystems have been subject to large biodiversity losses. We developed a Climate Change Sensitivity (CCS) indicator based on trait information for a selection of stream- and lake-dwelling Ephemeroptera, Plecoptera and Trichoptera taxa. We calculated the CCS scores based on ten species traits identified as sensitive to global climate change. We then assessed climate change sensitivity between the six main ecoregions of Sweden as well as the three Swedish regions based on Illies. This was done using biological data from 1, 382 stream and lake sites where we compared large-scale (ecoregional) patterns in climate change sensitivity with potential future exposure of these ecosystems to increased temperatures using ensemble-modelled future changes in air temperature. Current (1961~1990) measured temperature and ensemble-modelled future (2100) temperature showed an increase from the northernmost towards the southern ecoregions, whereas the predicted temperature change increased from south to north. The CCS indicator scores were highest in the two northernmost boreal ecoregions where we also can expect the largest global climate change-induced increase in temperature, indicating an unfortunate congruence of exposure and sensitivity to climate change. These results are of vital importance when planning and implementing management and conservation strategies in freshwater ecosystems, e.g., to mitigate increased temperatures using riparian buffer strips. We conclude that traits information on taxa specialization, e.g., in terms of feeding specialism or taxa having a preference for high altitudes as well as sensitivity to changes in temperature are important when assessing the risk from future global climate change to freshwater ecosystems.

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MIC-Drop: A platform for large-scale in vivo CRISPR screens

Science ◽

10.1126/science.abi8870 ◽

2021 ◽

pp. eabi8870

Author(s):

Saba Parvez ◽

Chelsea Herdman ◽

Manu Beerens ◽

Korak Chakraborti ◽

Zachary P. Harmer ◽

...

Keyword(s):

Large Scale ◽

Cultured Cells ◽

Cardiac Development ◽

Droplet Microfluidics ◽

Model Organisms ◽

Genetic Screens ◽

Large Numbers ◽

And Function ◽

Genome Scale

CRISPR-Cas9 can be scaled up for large-scale screens in cultured cells, but CRISPR screens in animals have been challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. Here, we report Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. The platform can efficiently identify genes responsible for morphological or behavioral phenotypes. In one application, we show MIC-Drop can identify small molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, we discover several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse-genetic screens in model organisms.

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The daunting polygenicity of mental illness: making a new map

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2017.0031 ◽

2018 ◽

Vol 373 (1742) ◽

pp. 20170031 ◽

Cited By ~ 18

Author(s):

Steven E. Hyman

Keyword(s):

Mental Health ◽

Large Scale ◽

Computational Models ◽

Model Organisms ◽

Human Biology ◽

Genetic Studies ◽

Computational Tools ◽

Experimental Systems ◽

Terra Incognita ◽

Phenotypic Complexity

An epochal opportunity to elucidate the pathogenic mechanisms of psychiatric disorders has emerged from advances in genomic technology, new computational tools and the growth of international consortia committed to data sharing. The resulting large-scale, unbiased genetic studies have begun to yield new biological insights and with them the hope that a half century of stasis in psychiatric therapeutics will come to an end. Yet a sobering picture is coming into view; it reveals daunting genetic and phenotypic complexity portending enormous challenges for neurobiology. Successful exploitation of results from genetics will require eschewal of long-successful reductionist approaches to investigation of gene function, a commitment to supplanting much research now conducted in model organisms with human biology, and development of new experimental systems and computational models to analyse polygenic causal influences. In short, psychiatric neuroscience must develop a new scientific map to guide investigation through a polygenic terra incognita . This article is part of a discussion meeting issue ‘Of mice and mental health: facilitating dialogue between basic and clinical neuroscientists’.

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An International Campaign for Agricultural and Livestock Genomics (CALG)

Asia-Pacific Biotech News ◽

10.1142/s0219030302001970 ◽

2002 ◽

Vol 06 (24) ◽

pp. 958-965

Author(s):

Jun Yu ◽

Jian Wang ◽

Huanming Yang

Keyword(s):

Large Scale ◽

Cost Effective ◽

Model Organisms ◽

Environmental Biology ◽

Cdna Sequences ◽

Governmental Agencies ◽

Technology Innovations ◽

A Genome ◽

Starting Point ◽

The Cost

A coordinated international effort to sequence agricultural and livestock genomes has come to its time. While human genome and genomes of many model organisms (related to human health and basic biological interests) have been sequenced or plugged in the sequencing pipelines, agronomically important crop and livestock genomes have not been given high enough priority. Although we are facing many challenges in policy-making, grant funding, regional task emphasis, research community consensus and technology innovations, many initiatives are being announced and formulated based on the cost-effective and large-scale sequencing procedure, known as whole genome shotgun (WGS) sequencing that produces draft sequences covering a genome from 95 percent to 99 percent. Identified genes from such draft sequences, coupled with other resources, such as molecular markers, large-insert clones and cDNA sequences, provide ample information and tools to further our knowledge in agricultural and environmental biology in the genome era that just comes to its accelerated period. If the campaign succeeds, molecular biologists, geneticists and field biologists from all countries, rich or poor, would be brought to the same starting point and expect another astronomical increase of basic genomic information, ready to convert effectively into knowledge that will ultimately change our lives and environment into a greater and better future. We call upon national and international governmental agencies and organizations as well as research foundations to support this unprecedented movement.

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Ecological Impacts of Megaprojects: Species Succession and Functional Composition

Plants ◽

10.3390/plants10112411 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2411

Author(s):

Hamada E. Ali ◽

Solveig Franziska Bucher

Keyword(s):

Plant Species ◽

Large Scale ◽

Invasive Plant ◽

Species Traits ◽

Natural Vegetation ◽

Ecological Impacts ◽

Imperata Cylindrica ◽

Dry Matter Content ◽

Large Scale Disturbance ◽

The Impact

Land-use changes have huge impacts on natural vegetation, especially megaprojects, as the vegetation layer is destroyed in the course of construction works affecting the plant community composition and functionality. This large-scale disturbance might be a gateway for the establishment of invasive plant species, which can outcompete the natural flora. In contrast, species occurring in the area before the construction are not able to re-establish. In this study, we analyzed the impact of a pipeline construction on a wetland nature reserve located in northern Egypt. Therefore, we analyzed the plant species occurrence and abundance and measured each plant species’ traits before the construction in 2017 as well as on multiple occasions up to 2 years after the construction had finished on altogether five sampling events. We found that the construction activity led to the establishment of an invasive species which previously did not occur in the area, namely, Imperata cylindrica, whereas five species (Ipomoea carnea, Pluchea dioscoridis, Polygonum equisetiforme, Tamarix nilotica, and Typha domingensis) could not re-establish after the disturbance. The functionality of ecosystems assessed via the analysis of plant functional traits (plant height, specific leaf area, and leaf dry matter content) changed within species over all sampling events and within the community showing a tendency to approximate pre-construction values. Functional dispersion and Rao’s quadratic diversity were higher after the megaproject than before. These findings are important to capture possible re-establishment and recovery of natural vegetation after construction and raise awareness to the impact of megaprojects, especially in areas which are high priority for conservation.

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Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

10.1101/469569 ◽

2018 ◽

Author(s):

Valerie Wood ◽

Antonia Lock ◽

Midori A. Harris ◽

Kim Rutherford ◽

Jürg Bähler ◽

...

Keyword(s):

Gene Ontology ◽

Fission Yeast ◽

Genome Sequencing ◽

Large Scale ◽

Biological Process ◽

Blind Spot ◽

Model Organisms ◽

Biological Processes ◽

Health And Disease

AbstractThe first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

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Phyletic distribution and diversification of the Phage Shock Protein stress response system in bacteria and archaea

10.1101/2021.02.15.431232 ◽

2021 ◽

Author(s):

Philipp F. Popp ◽

Vadim M. Gumerov ◽

Ekaterina P. Andrianova ◽

Lisa Bewersdorf ◽

Thorsten Mascher ◽

...

Keyword(s):

Stress Response ◽

Large Scale ◽

Cell Envelope ◽

Model Organisms ◽

Microbial World ◽

Natural Classification ◽

Response System ◽

Core Proteins ◽

Envelope Stress

AbstractThe bacterial cell envelope is an essential structure that protects the cell from environmental threats, while simultaneously serving as communication interface and diffusion barrier. Therefore, maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protection networks that connect stress perception, transmembrane signal transduction and mediation of cellular responses upon cell envelope stress. The phage shock protein (PSP) stress response is one of such conserved protection networks. Most of the knowledge about the Psp response comes from studies in the Gram-negative model bacterium, Escherichia coli where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of Proteobacteria, Actinobacteria, and Firmicutes; however, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and demonstrated that the PSP system deviates dramatically from the proteobacterial prototype. Two of its core proteins, PspA and PspC, have been integrated in various (often phylum-specifically) conserved protein networks during evolution. Based on protein sequence and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system of PSP networks in bacteria and archaea. We performed a comprehensive in vivo protein interaction screen for the PSP network newly identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected PSP response system, illustrating the validity of our approach. Our study highlights the diversity of PSP organization and function across many bacterial and archaeal phyla and will serve as foundation for future studies of this envelope stress response beyond model organisms.

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Deconstructing Gastrulation at the Single Cell Level

10.1101/2021.09.16.460711 ◽

2021 ◽

Author(s):

Tomer Stern ◽

Sebastian J Streichan ◽

Stanislav Y Shvartsman ◽

Eric F Wieschaus

Keyword(s):

Large Scale ◽

Drosophila Embryo ◽

Cell Segmentation ◽

Model Organisms ◽

Specific Cell ◽

Cell Behaviors ◽

Animal Development ◽

Wide Range ◽

Cell Groups ◽

Epithelial Sheets

Gastrulation movements in all animal embryos start with regulated deformations of patterned epithelial sheets. Current studies of gastrulation use a wide range of model organisms and emphasize either large-scale tissue processes or dynamics of individual cells and cell groups. Here we take a step towards bridging these complementary strategies and deconstruct early stages of gastrulation in the entire Drosophila embryo, where transcriptional patterns in the blastoderm give rise to region-specific cell behaviors. Our approach relies on an integrated computational framework for cell segmentation and tracking and on efficient algorithms for event detection. Our results reveal how thousands of cell shape changes, divisions, and intercalations drive large-scale deformations of the patterned blastoderm, setting the stage for systems-level dissection of a pivotal step in animal development.

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iProteinDB: an integrative database of Drosophila post-translational modifications

10.1101/386268 ◽

2018 ◽

Cited By ~ 2

Author(s):

Yanhui Hu ◽

Richelle Sopko ◽

Verena Chung ◽

Romain A. Studer ◽

Sean D. Landry ◽

...

Keyword(s):

Protein Interactions ◽

Protein Function ◽

Large Scale ◽

Model Organisms ◽

General Strategy ◽

Post Translational Modification ◽

Post Translational Modifications ◽

Functional Sites ◽

Evolutionarily Conserved ◽

And Function

AbstractPost-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing stability, protein interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, commonly serine, threonine and tyrosine. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that many phosphorylation sites may be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites with regards to regulation and function. To facilitate the identification of conserved phosphosites, we generated a large-scale phosphoproteomics dataset from Drosophila embryos collected from six closely-related species. We built iProteinDB (https://www.flyrnai.org/tools/iproteindb/), a resource integrating these data with other high-throughput PTM datasets, including vertebrates, and manually curated information for Drosophila. At iProteinDB, scientists can view the PTM landscape for any Drosophila protein and identify predicted functional phosphosites based on a comparative analysis of data from closely-related Drosophila species. Further, iProteinDB enables comparison of PTM data from Drosophila to that of orthologous proteins from other model organisms, including human, mouse, rat, Xenopus laevis, Danio rerio, and Caenorhabditis elegans.

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Body size information in large-scale acoustic bat databases

PeerJ ◽

10.7717/peerj.5370 ◽

2018 ◽

Vol 6 ◽

pp. e5370 ◽

Cited By ~ 4

Author(s):

Caterina Penone ◽

Christian Kerbiriou ◽

Jean-François Julien ◽

Julie Marmet ◽

Isabelle Le Viol

Keyword(s):

Body Size ◽

Large Scale ◽

Principal Component ◽

Acoustic Signals ◽

Species Traits ◽

Climatic Variables ◽

Characteristic Frequencies ◽

Acoustic Data ◽

Forearm Length ◽

Broad Scale

Background Citizen monitoring programs using acoustic data have been useful for detecting population and community patterns. However, they have rarely been used to study broad scale patterns of species traits. We assessed the potential of acoustic data to detect broad scale patterns in body size. We compared geographical patterns in body size with acoustic signals in the bat species Pipistrellus pipistrellus. Given the correlation between body size and acoustic characteristics, we expected to see similar results when analyzing the relationships of body size and acoustic signals with climatic variables. Methods We assessed body size using forearm length measurements of 1,359 bats, captured by mist nets in France. For acoustic analyses, we used an extensive dataset collected through the French citizen bat survey. We isolated each bat echolocation call (n = 4,783) and performed automatic measures of signals, including the frequency of the flattest part of the calls (characteristic frequency). We then examined the relationship between forearm length, characteristic frequencies, and two components resulting from principal component analysis for geographic (latitude, longitude) and climatic variables. Results Forearm length was positively correlated with higher precipitation, lower seasonality, and lower temperatures. Lower characteristic frequencies (i.e., larger body size) were mostly related to lower temperatures and northern latitudes. While conducted on different datasets, the two analyses provided congruent results. Discussion Acoustic data from citizen science programs can thus be useful for the detection of large-scale patterns in body size. This first analysis offers a new perspective for the use of large acoustic databases to explore biological patterns and to address both theoretical and applied questions.

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