scholarly journals Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

2012 ◽  
Vol 279 (1735) ◽  
pp. 1873-1882 ◽  
Author(s):  
Brooks E. Miner ◽  
Luc De Meester ◽  
Michael E. Pfrender ◽  
Winfried Lampert ◽  
Nelson G. Hairston
Keyword(s):  
Evolutionary Dynamics ◽  
Model System ◽  
Causal Chain ◽  
Ecosystem Dynamics ◽  
Model Organisms ◽  
Ecological Interactions ◽  
Evolutionary Changes ◽  
Genomic Tools ◽  
Biological Hierarchy ◽  
Modern Genomic

How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances.

scholarly journals Brown Algal Model Organisms

2020 ◽  
Vol 54 (1) ◽  
pp. 71-92
Author(s):  
Susana M. Coelho ◽  
J. Mark Cock
Keyword(s):  
Novel Species ◽  
Classical Model ◽  
Saccharina Japonica ◽  
Model System ◽  
Model Organisms ◽  
Phylogenetic Groups ◽  
The Past ◽  
Genomic Tools ◽  
Modern Genomic ◽  
Multicellular Organisms

Model organisms are extensively used in research as accessible and convenient systems for studying a particular area or question in biology. Traditionally, only a limited number of organisms have been studied in detail, but modern genomic tools are enabling researchers to extend beyond the set of classical model organisms to include novel species from less-studied phylogenetic groups. This review focuses on model species for an important group of multicellular organisms, the brown algae. The development of genetic and genomic tools for the filamentous brown alga Ectocarpus has led to it emerging as a general model system for this group, but additional models, such as Fucus or Dictyota dichotoma, remain of interest for specific biological questions. In addition, Saccharina japonica has emerged as a model system to directly address applied questions related to algal aquaculture. We discuss the past, present, and future of brown algal model organisms in relation to the opportunities and challenges in brown algal research.

scholarly journals Genomics in the ecological arena

2010 ◽  
Vol 7 (1) ◽  
pp. 2-3 ◽  
Author(s):  
Luisa Orsini ◽  
Ellen Decaestecker ◽  
Luc De Meester ◽  
Michael E. Pfrender ◽  
John K. Colbourne
Keyword(s):  
Model System ◽  
Model Organisms ◽  
Meeting Report ◽  
Model Species ◽  
Environmental Genomics ◽  
Large Community ◽  
Genomic Tools ◽  
The Times ◽  
First Time ◽  
European University

This meeting report presents the cutting-edge research that is developing around the waterflea Daphnia , an emerging model system in environmental genomics. Daphnia has been a model species in ecology, toxicology and evolution for many years and is supported by a large community of ecologists, evolutionary biologists and ecotoxicologists. Thanks to new advances in genomics and transciptomics and to the sustained efforts of the Daphnia Genomics Consortium (DGC), Daphnia is also rapidly developing as a model system in environmental genomics. Advances in this emerging field were presented at the DGC 2010, held for the first time in a European University. During the meeting, a plethora of elegant studies were presented on the mechanisms of responses to environmental challenges using recently developed genomic tools. The DGC 2010 is a concrete example of the new trends in ecology and evolution. The times are mature for the application of innovative genomic and transcriptomic tools for studies of environmental genomics in non-model organisms.

scholarly journals Research on Plants for the Understanding of Diseases of Nuclear and Mitochondrial Origin

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Claudia P. Spampinato ◽  
Diego F. Gomez-Casati
Keyword(s):  
Current Knowledge ◽  
Model System ◽  
Human Diseases ◽  
Model Organisms ◽  
Human Cell Lines ◽  
Molecular Defects ◽  
Human Genes ◽  
Clinical Disorders ◽  
Mitochondrial Origin ◽  
Experimental Findings

Different model organisms, such asEscherichia coli,Saccharomyces cerevisiae,Caenorhabditis elegans,Drosophila melanogaster, mouse, cultured human cell lines, among others, were used to study the mechanisms of several human diseases. Since human genes and proteins have been structurally and functionally conserved in plant organisms, the use of plants, especiallyArabidopsis thaliana, as a model system to relate molecular defects to clinical disorders has recently increased. Here, we briefly review our current knowledge of human diseases of nuclear and mitochondrial origin and summarize the experimental findings of plant homologs implicated in each process.

scholarly journals Eco-evolutionary dynamics

2009 ◽  
Vol 364 (1523) ◽  
pp. 1483-1489 ◽  
Author(s):  
F. Pelletier ◽  
D. Garant ◽  
A.P. Hendry
Keyword(s):  
Time Scale ◽  
Evolutionary Dynamics ◽  
Evolutionary Change ◽  
Ecological Change ◽  
Evolutionary Changes ◽  
Microevolutionary Change ◽  
Theoretical Developments ◽  
Rapid Evolutionary Change

Evolutionary ecologists and population biologists have recently considered that ecological and evolutionary changes are intimately linked and can occur on the same time-scale. Recent theoretical developments have shown how the feedback between ecological and evolutionary dynamics can be linked, and there are now empirical demonstrations showing that ecological change can lead to rapid evolutionary change. We also have evidence that microevolutionary change can leave an ecological signature. We are at a stage where the integration of ecology and evolution is a necessary step towards major advances in our understanding of the processes that shape and maintain biodiversity. This special feature about ‘eco-evolutionary dynamics’ brings together biologists from empirical and theoretical backgrounds to bridge the gap between ecology and evolution and provide a series of contributions aimed at quantifying the interactions between these fundamental processes.

scholarly journals AN OIL SPILL MODEL SYSTEM FOR ARCTIC WATERS

1989 ◽  
Vol 1989 (1) ◽  
pp. 517-523
Author(s):  
Malcolm Spaulding ◽  
Tatsusaburo Isaji ◽  
Katherine Jayko
Keyword(s):  
Oil Spill ◽  
Sensitivity Study ◽  
Model System ◽  
Ecosystem Dynamics ◽  
Environmental Data ◽  
Trajectory Data ◽  
Duration Distribution ◽  
Coastal Sea ◽  
Model Components

ABSTRACT An Arctic coastal sea model system, consisting of submodels for weather, hydrodynamics, waves, suspended sediment, ice cover, oil spill trajectory and fates, and ecosystem dynamics is presented. The structure and operation of each sub-model and linkages among the various model components are briefly described. The weather, hydrodynamic, ice, and oil spill fates components of the model system are applied to predict hydrodynamics and oil spill trajectories from selected release points in the Bering Sea. Trajectory data are analyzed to describe the percent of trajectories affecting land and the direction, length, and duration distribution of trajectories. A detailed sensitivity study is performed to determine the role of the various mean current components and wind drift effects in describing spill trajectories. Model predictions highlight the importance of accurately representing the environmental data used as input to the model.

Daphnia as a Model for Eco-evolutionary Dynamics

2018 ◽  
pp. 403-424
Author(s):  
Matthew R. Walsh ◽  
Michelle Packer ◽  
Shannon Beston ◽  
Collin Funkhouser ◽  
Michael Gillis ◽  
...  
Keyword(s):  
Life History ◽  
Evolutionary Dynamics ◽  
Model Organism ◽  
Life History Evolution ◽  
Ecological Processes ◽  
Evolutionary Forces ◽  
Evolutionary Changes ◽  
History Evolution ◽  
Ecological Importance ◽  
The Many

Much research has shown that variation in ecological processes can drive rapid evolutionary changes over periods of years to decades. Such contemporary adaptation sets the stage for evolution to have reciprocal impacts on the properties of populations, communities, and ecosystems, with ongoing interactions between ecological and evolutionary forces. The importance and generality of these eco-evolutionary dynamics are largely unknown. In this chapter, we promote the use of water fleas (Daphnia sp.) as a model organism in the exploration of eco-evolutionary interactions in nature. The many characteristics of Daphnia that make them suitable for laboratory study in conjunction with their well-known ecological importance in lakes, position Daphnia to contribute new and important insights into eco-evolutionary dynamics. We first review the influence of key environmental stressors in Daphnia evolution. We then highlight recent work documenting the pathway from life history evolution to ecology using Daphnia as a model. This review demonstrates that much is known about the influence of ecology on Daphnia life history evolution, while research exploring the genomic basis of adaptation as well as the influence of Daphnia life history traits on ecological processes is beginning to accumulate.

Heritability, polymorphism, and population dynamics: individual-based eco-evolutionary simulations

2021 ◽  
pp. 329-340
Author(s):  
Anna Kuparinen
Keyword(s):  
Population Dynamics ◽  
Life Histories ◽  
Evolutionary Dynamics ◽  
Atlantic Cod ◽  
Population Projections ◽  
Phenotypic Traits ◽  
Evolutionary Changes ◽  
Future Challenges ◽  
Evolutionary Simulations ◽  
Main Message

Contemporary evolution that occurs across ecologically relevant time scales, such as a few generations or decades, can not only change phenotypes but also feed back to demographic parameters and the dynamics of populations. This chapter presents a method to make phenotypic traits evolve in mechanistic individual-based simulations. The method is broadly applicable, as demonstrated through its applications to boreal forest adaptation to global warming, eco-evolutionary dynamics driven by fishing-induced selection in Atlantic cod, and the evolution of age at maturity in Atlantic salmon. The main message of this chapter is that there may be little reason to exclude phenotypic evolution in analyses of population dynamics, as these can be modified by evolutionary changes in life histories. Future challenges will be to integrate rapidly accumulating genomic knowledge and an ecosystem perspective to improve population projections and to better understand the drivers of population dynamics.

Lessons from Worm Dendritic Patterning

2019 ◽  
Vol 42 (1) ◽  
pp. 365-383 ◽  
Author(s):  
Sharon Inberg ◽  
Anna Meledin ◽  
Veronika Kravtsov ◽  
Yael Iosilevskii ◽  
Meital Oren-Suissa ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Animal Model ◽  
Light And Electron Microscopy ◽  
Dendritic Tree ◽  
Model System ◽  
Model Organisms ◽  
Structural Units ◽  
The Past ◽  
Structural And Functional Properties ◽  
Made In

The structural and functional properties of neurons have intrigued scientists since the pioneering work of Santiago Ramón y Cajal. Since then, emerging cutting-edge technologies, including light and electron microscopy, electrophysiology, biochemistry, optogenetics, and molecular biology, have dramatically increased our understanding of dendritic properties. This advancement was also facilitated by the establishment of different animal model organisms, from flies to mammals. Here we describe the emerging model system of a Caenorhabditis elegans polymodal neuron named PVD, whose dendritic tree follows a stereotypical structure characterized by repeating candelabra-like structural units. In the past decade, progress has been made in understanding PVD's functions, morphogenesis, regeneration, and aging, yet many questions still remain.

scholarly journals Modern Genomic Tools for Pigeonpea Improvement: Status and Prospects

2017 ◽  
pp. 41-54 ◽  
Author(s):  
Abhishek Bohra ◽  
Shalini Pareek ◽  
Rintu Jha ◽  
Rachit K. Saxena ◽  
Indra P. Singh ◽  
...  
Keyword(s):  
Genomic Tools ◽  
Modern Genomic

scholarly journals De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 305 ◽  
Author(s):  
Mark P Peterson ◽  
Danielle J Whittaker ◽  
Shruthi Ambreth ◽  
Suhas Sureshchandra ◽  
Aaron Buechlein ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Ecological Model ◽  
De Novo ◽  
Model System ◽  
Junco Hyemalis ◽  
De Novo Transcriptome ◽  
Genomic Tools ◽  
De Novo Transcriptome Sequencing ◽  
Ecological Model System
Sign in / Sign up

Export Citation Format

Share Document