scholarly journals Threespine Stickleback: A Model System For Evolutionary Genomics

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kerry Reid ◽  
Michael A. Bell ◽  
Krishna R. Veeramah
Keyword(s):  
Complex Traits ◽  
Model System ◽  
Threespine Stickleback ◽  
Evolutionary Genomics ◽  
Phenotypic Traits ◽  
Publication Date ◽  
Small Fish ◽  
Wide Range ◽  
Threespine Sticklebacks ◽  
Genomic Basis

The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host–microbiome and host–parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 426 ◽  
Author(s):  
Daniel Berner ◽  
Marius Roesti ◽  
Steven Bilobram ◽  
Simon K. Chan ◽  
Heather Kirk ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Gene Annotation ◽  
Model System ◽  
Threespine Stickleback ◽  
Evolutionary Genomics ◽  
Digital Repository ◽  
High Quality ◽  
De Novo Gene ◽  
Dna Libraries

The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7).

scholarly journals Genome Characterization, Prevalence, and Transmission Mode of a Novel Picornavirus Associated with the Threespine Stickleback Fish (Gasterosteus aculeatus)

2019 ◽  
Vol 93 (9) ◽  
Author(s):  
Megan A. Hahn ◽  
Nolwenn M. Dheilly
Keyword(s):  
Gasterosteus Aculeatus ◽  
Rna Virus ◽  
Wide Distribution ◽  
Model System ◽  
Threespine Stickleback ◽  
Tissue Samples ◽  
Content Type ◽  
Threespine Sticklebacks ◽  
The Impact

ABSTRACT The complete genome sequence of an RNA virus was assembled from RNA sequencing of virus particles purified from threespine stickleback intestine tissue samples. This new virus is most closely related to the Eel picornavirus and can be assigned to the genus Potamipivirus in the family Picornaviridae. Its unique genetic properties are enough to establish a new species, dubbed the Threespine Stickleback picornavirus (TSPV). Due to their broad geographic distribution throughout the Northern Hemisphere and parallel adaptation to freshwater, threespine sticklebacks have become a model in evolutionary ecology. Further analysis using diagnostic PCRs revealed that TSPV is highly prevalent in both anadromous and freshwater populations of threespine sticklebacks, infects almost all fish tissues, and is transmitted vertically to offspring obtained from in vitro fertilization in laboratory settings. Finally, TSPV was found in Sequence Reads Archives of transcriptome of Gasterosteus aculeatus, further demonstrating its wide distribution and unsought prevalence in samples. It is thus necessary to test the impact of TSPV on the biology of threespine sticklebacks, as this widespread virus could interfere with the behavioral, physiological, or immunological studies that employ this fish as a model system. IMPORTANCE The threespine stickleback species complex is an important model system in ecological and evolutionary studies because of the large number of isolated divergent populations that are experimentally tractable. For similar reasons, its coevolution with the cestode parasite Schistocephalus solidus, its interaction with gut microbes, and the evolution of its immune system are of growing interest. Herein we describe the discovery of an RNA virus that infects both freshwater and anadromous populations of sticklebacks. We show that the virus is transmitted vertically in laboratory settings and found it in Sequence Reads Archives, suggesting that experiments using sticklebacks were conducted in the presence of the virus. This discovery can serve as a reminder that the presence of viruses in wild-caught animals is possible, even when animals appear healthy. Regarding threespine sticklebacks, the impact of Threespine Stickleback picornavirus (TSPV) on the fish biology should be investigated further to ensure that it does not interfere with experimental results.

scholarly journals Machine Learning models identify gene predictors of waggle dance behaviour in honeybees

2021 ◽  
Author(s):  
Marcell Veiner ◽  
Juliano Morimoto ◽  
Elli Leadbeater ◽  
Fabio Manfredini
Keyword(s):  
Machine Learning ◽  
Evolutionary Ecology ◽  
Waggle Dance ◽  
Phenotypic Traits ◽  
Hnrnp A1 ◽  
Wide Range ◽  
Transcriptomics Data ◽  
Differential Gene ◽  
G Protein Coupled ◽  
Genomic Basis

The molecular characterisation of complex behaviours is a challenging task as a range of different factors are often involved to produce the observed phenotype. An established approach is to look at the overall levels of expression of brain genes – known as ‘neurogenomics’ – to select the best candidates that associate with patterns of interest. This approach has relied so far on a set of powerful statistical tools capable to provide a snapshot of the expression of many thousands of genes that are present in an organism’s genome. However, traditional neurogenomic analyses have some well-known limitations; above all, the limited number of biological replicates compared to the number of genes tested – often referred to as “curse of dimensionality”. Here we implemented a new Machine Learning (ML) approach that can be used as a complement to established methods of transcriptomic analyses. We tested three types of ML models for their performance in the identification of genes associated with honeybee waggle dance. We then intersected the results of these analyses with traditional outputs of differential gene expression analyses and identified two promising candidates for the neural regulation of the waggle dance: the G-protein coupled receptor boss and hnRNP A1, a gene involved in alternative splicing. Overall, our study demonstrates the application of Machine Learning to analyse transcriptomics data and identify genes underlying social behaviour. This approach has great potential for application to a wide range of different scenarios in evolutionary ecology, when investigating the genomic basis for complex phenotypic traits.

scholarly journals Diversity and sexual dimorphism in the head lateral line system in North Sea populations of threespine sticklebacks, Gasterosteus aculeatus (Teleostei: Gasterosteidae)

Zoomorphology ◽  
2020 ◽  
Author(s):  
Harald Ahnelt ◽  
David Ramler ◽  
Maria Ø. Madsen ◽  
Lasse F. Jensen ◽  
Sonja Windhager
Keyword(s):  
Sexual Dimorphism ◽  
North Sea ◽  
Lateral Line ◽  
Gasterosteus Aculeatus ◽  
Sensory System ◽  
Threespine Stickleback ◽  
Lateral Line System ◽  
Line System ◽  
Marine Population ◽  
Threespine Sticklebacks

AbstractThe mechanosensory lateral line of fishes is a flow sensing system and supports a number of behaviors, e.g. prey detection, schooling or position holding in water currents. Differences in the neuromast pattern of this sensory system reflect adaptation to divergent ecological constraints. The threespine stickleback, Gasterosteus aculeatus, is known for its ecological plasticity resulting in three major ecotypes, a marine type, a migrating anadromous type and a resident freshwater type. We provide the first comparative study of the pattern of the head lateral line system of North Sea populations representing these three ecotypes including a brackish spawning population. We found no distinct difference in the pattern of the head lateral line system between the three ecotypes but significant differences in neuromast numbers. The anadromous and the brackish populations had distinctly less neuromasts than their freshwater and marine conspecifics. This difference in neuromast number between marine and anadromous threespine stickleback points to differences in swimming behavior. We also found sexual dimorphism in neuromast number with males having more neuromasts than females in the anadromous, brackish and the freshwater populations. But no such dimorphism occurred in the marine population. Our results suggest that the head lateral line of the three ecotypes is under divergent hydrodynamic constraints. Additionally, sexual dimorphism points to divergent niche partitioning of males and females in the anadromous and freshwater but not in the marine populations. Our findings imply careful sampling as an important prerequisite to discern especially between anadromous and marine threespine sticklebacks.

scholarly journals The utility of a closed breeding colony of Peromyscus leucopus for dissecting complex traits

2021 ◽  
Author(s):  
Anthony D Long ◽  
Alan Barbour ◽  
Phillip N Long ◽  
Vanessa J Cook ◽  
Arundhati Majumder
Keyword(s):  
Complex Traits ◽  
Genetic Model ◽  
Peromyscus Leucopus ◽  
False Positive Rate ◽  
Model System ◽  
Sequencing Data ◽  
Power Estimate ◽  
Genome Wide ◽  
Low Pass ◽  
Closed Colony

Although Peromyscus leucopus (deermouse) is not considered a genetic model system, its genus is well suited for addressing several questions of biologist interest, including the genetic bases of longevity, behavior, physiology, adaptation, and its ability to serve as a disease vector. Here we explore a diversity outbred approach for dissecting complex traits in Peromyscus leucopus, a non-traditional genetic model system. We take advantage of a closed colony of deer-mice founded from 38 individuals between 1982 and 1985 and subsequently maintained for 35+ years (~40-60 generations). From 405 low-pass (~1X) short-read sequenced deermice we accurately imputed genotypes at 17,751,882 SNPs. Conditional on observed genotypes for a subset of 297 individuals, simulations were conducted in which a QTL contributes 5% to a complex trait under three different genetic models. The power of either a haplotype- or marker-based statistical test was estimated to be 15-25% to detect the hidden QTL. Although modest, this power estimate is consistent with that of DO/HS mice and rat experiments for an experiment with ~300 individuals. This limitation in QTL detection is mostly associated with the stringent significance threshold required to hold the genome-wide false positive rate low, as in all cases we observe considerable linkage signal at the location of simulated QTL, suggesting a larger panel would exhibit greater power. For the subset of cases where a QTL was detected, localization ability appeared very desirable at ~1-2Mb. We finally carried out a GWAS on a demonstration trait, bleeding time. No tests exceeded the threshold for genome-wide significance, but one of four suggestive regions co-localizes with Von Willebrand factor. Our work suggests that complex traits can be dissected in founders-unknown P. leucopus colony mice in much the same manner as founders-known DO/HS mice and rats, with genotypes obtained from low pass sequencing data. Our results further suggest that the DO/HS approach can be powerfully extended to any system in which a founders-unknown closed colony has been maintained for several dozen generations.

scholarly journals Strategies to Increase Prediction Accuracy in Genomic Selection of Complex Traits in Alfalfa (Medicago sativa L.)

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3372
Author(s):  
Cesar A. Medina ◽  
Harpreet Kaur ◽  
Ian Ray ◽  
Long-Xi Yu
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Medicago Sativa ◽  
Genomic Selection ◽  
Complex Traits ◽  
Prediction Accuracy ◽  
Breeding Value ◽  
Phenotypic Traits ◽  
Genome Wide ◽  
Medicago Sativa L

Agronomic traits such as biomass yield and abiotic stress tolerance are genetically complex and challenging to improve through conventional breeding approaches. Genomic selection (GS) is an alternative approach in which genome-wide markers are used to determine the genomic estimated breeding value (GEBV) of individuals in a population. In alfalfa (Medicago sativa L.), previous results indicated that low to moderate prediction accuracy values (<70%) were obtained in complex traits, such as yield and abiotic stress resistance. There is a need to increase the prediction value in order to employ GS in breeding programs. In this paper we reviewed different statistic models and their applications in polyploid crops, such as alfalfa and potato. Specifically, we used empirical data affiliated with alfalfa yield under salt stress to investigate approaches that use DNA marker importance values derived from machine learning models, and genome-wide association studies (GWAS) of marker-trait association scores based on different GWASpoly models, in weighted GBLUP analyses. This approach increased prediction accuracies from 50% to more than 80% for alfalfa yield under salt stress. Finally, we expended the weighted GBLUP approach to potato and analyzed 13 phenotypic traits and obtained similar results. This is the first report on alfalfa to use variable importance and GWAS-assisted approaches to increase the prediction accuracy of GS, thus helping to select superior alfalfa lines based on their GEBVs.

scholarly journals Prediction of Commuter’s Daily Time Allocation

2013 ◽  
Vol 25 (5) ◽  
pp. 445-455 ◽  
Author(s):  
Fang Zong ◽  
Jia Hongfei ◽  
Pan Xiang ◽  
Wu Yang
Keyword(s):  
Support Vector Regression ◽  
Travel Time ◽  
Time Allocation ◽  
Prediction Accuracy ◽  
Travel Demand ◽  
Model System ◽  
Support Vector ◽  
Activity Duration ◽  
Wide Range ◽  
Duration Prediction

This paper presents a model system to predict the time allocation in commuters’ daily activity-travel pattern. The departure time and the arrival time are estimated with Ordered Probit model and Support Vector Regression is introduced for travel time and activity duration prediction. Applied in a real-world time allocation prediction experiment, the model system shows a satisfactory level of prediction accuracy. This study provides useful insights into commuters’ activity-travel time allocation decision by identifying the important influences, and the results are readily applied to a wide range of transportation practice, such as travel information system, by providing reliable forecast for variations in travel demand over time. By introducing the Support Vector Regression, it also makes a methodological contribution in enhancing prediction accuracy of travel time and activity duration prediction.

The Basis of Navigation Across Species

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Cody A. Freas ◽  
Ken Cheng
Keyword(s):  
Large Scale ◽  
Error Reduction ◽  
Annual Review ◽  
Publication Date ◽  
Additional Component ◽  
Oscillatory Systems ◽  
Neural Architecture ◽  
Wide Range ◽  
Reduction Strategies ◽  
Cycling Behavior

Animals navigate a wide range of distances, from a few millimeters to globe-spanning journeys of thousands of kilometers. Despite this array of navigational challenges, similar principles underlie these behaviors across species. Here, we focus on the navigational strategies and supporting mechanisms in four well-known systems: the large-scale migratory behaviors of sea turtles and lepidopterans as well as navigation on a smaller scale by rats and solitarily foraging ants. In lepidopterans, rats, and ants we also discuss the current understanding of the neural architecture which supports navigation. The orientation and navigational behaviors of these animals are defined in terms of behavioral error-reduction strategies reliant on multiple goal-directed servomechanisms. We conclude by proposing to incorporate an additional component into this system: the observation that servomechanisms operate on oscillatory systems of cycling behavior. These oscillators and servomechanisms comprise the basis for directed orientation and navigational behaviors. Expected final online publication date for the Annual Review of Psychology, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Engineering Advances in Spray Drying for Pharmaceuticals

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
John M. Baumann ◽  
Molly S. Adam ◽  
Joel D. Wood
Keyword(s):  
Spray Drying ◽  
Oral Delivery ◽  
Process Development ◽  
Solid Dispersions ◽  
Amorphous Solid ◽  
Annual Review ◽  
Publication Date ◽  
Dry Powders ◽  
Wide Range ◽  
Pharmaceutical Industries

Spray drying is a versatile technology that has been applied widely in the chemical, food, and, most recently, pharmaceutical industries. This review focuses on engineering advances and the most significant applications of spray drying for pharmaceuticals. An in-depth view of the process and its use is provided for amorphous solid dispersions, a major, growing drug-delivery approach. Enhanced understanding of the relationship of spray-drying process parameters to final product quality attributes has made robust product development possible to address a wide range of pharmaceutical problem statements. Formulation and process optimization have leveraged the knowledge gained as the technology has matured, enabling improved process development from early feasibility screening through commercial applications. Spray drying's use for approved small-molecule oral products is highlighted, as are emerging applications specific to delivery of biologics and non-oral delivery of dry powders. Based on the changing landscape of the industry, significant future opportunities exist for pharmaceutical spray drying. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 12 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Chemical Stability of Proteins in Foods: Oxidation and the Maillard Reaction

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Mahesha M. Poojary ◽  
Marianne N. Lund
Keyword(s):  
Maillard Reaction ◽  
Protein Oxidation ◽  
Oxidation Products ◽  
Protein Carbonyls ◽  
Annual Review ◽  
Publication Date ◽  
Food Protein ◽  
Food Proteins ◽  
Wide Range ◽  
Specific Oxidation

Protein is a major nutrient present in foods along with carbohydrates and lipids. Food proteins undergo a wide range of modifications during food production, processing, and storage. In this review, we discuss two major reactions, oxidation and the Maillard reaction, involved in chemical modifications of food proteins. Protein oxidation in foods is initiated by metal-, enzyme-, or light-induced processes. Food protein oxidation results in the loss of thiol groups and the formation of protein carbonyls and specific oxidation products of cysteine, tyrosine, tryptophan, phenylalanine, and methionine residues, such as disulfides, dityrosine, kynurenine, m-tyrosine, and methionine sulfoxide. The Maillard reaction involves the reaction of nucleophilic amino acid residues with reducing sugars, which yields numerous heterogeneous compounds such as α-dicarbonyls, furans, Strecker aldehydes, advanced glycation end-products, and melanoidins. Both protein oxidation and the Maillard reaction result in the loss of essential amino acids but may positively or negatively impact food structure and flavor. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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