Prevalence and Adaptive Impact of Introgression

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Nathaniel B. Edelman ◽  
James Mallet
Keyword(s):  
Genetic Variation ◽  
Adaptive Evolution ◽  
Genetic Variants ◽  
Genomic Data ◽  
Annual Review ◽  
Publication Date ◽  
Adaptive Introgression ◽  
Changing Environments ◽  
Potential Benefits

Alleles that introgressed between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays

2021 ◽  
Vol 62 (1) ◽  
Author(s):  
Renee C. Geck ◽  
Gabriel Boyle ◽  
Clara J. Amorosi ◽  
Douglas M. Fowler ◽  
Maitreya J. Dunham
Keyword(s):  
Next Generation Sequencing ◽  
Functional Data ◽  
Genetic Variants ◽  
Genetic Information ◽  
Annual Review ◽  
Publication Date ◽  
Drug Selection ◽  
Functional Consequences ◽  
Pharmacology And Toxicology ◽  
Generation Sequencing

As costs of next-generation sequencing decrease, identification of genetic variants has far outpaced our ability to understand their functional consequences. This lack of understanding is a central challenge to a key promise of pharmacogenomics: using genetic information to guide drug selection and dosing. Recently developed multiplexed assays of variant effect enable experimental measurement of the function of thousands of variants simultaneously. Here, we describe multiplexed assays that have been performed on nearly 25,000 variants in eight key pharmacogenes ( ADRB2, CYP2C9, CYP2C19, NUDT15, SLCO1B1, TMPT, VKORC1, and the LDLR promoter), discuss advances in experimental design, and explore key challenges that must be overcome to maximize the utility of multiplexed functional data. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Perspectives on Allele-Specific Expression

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Siobhan Cleary ◽  
Cathal Seoighe
Keyword(s):  
Gene Expression ◽  
Genetic Variants ◽  
Data Science ◽  
Genetic Diseases ◽  
Annual Review ◽  
Publication Date ◽  
Biomedical Data ◽  
Specific Expression ◽  
Cis Acting ◽  
Gene Copies

Diploidy has profound implications for population genetics and susceptibility to genetic diseases. Although two copies are present for most genes in the human genome, they are not necessarily both active or active at the same level in a given individual. Genomic imprinting, resulting in exclusive or biased expression in favor of the allele of paternal or maternal origin, is now believed to affect hundreds of human genes. A far greater number of genes display unequal expression of gene copies due to cis-acting genetic variants that perturb gene expression. The availability of data generated by RNA sequencing applied to large numbers of individuals and tissue types has generated unprecedented opportunities to assess the contribution of genetic variation to allelic imbalance in gene expression. Here we review the insights gained through the analysis of these data about the extent of the genetic contribution to allelic expression imbalance, the tools and statistical models for gene expression imbalance, and what the results obtained reveal about the contribution of genetic variants that alter gene expression to complex human diseases and phenotypes. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 4 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Tamar Schlick ◽  
Stephanie Portillo-Ledesma ◽  
Christopher G. Myers ◽  
Lauren Beljak ◽  
Justin Chen ◽  
...  
Keyword(s):  
Modeling And Simulation ◽  
Annual Review ◽  
Publication Date ◽  
Long Term Effects ◽  
Short Term ◽  
Biomolecular Modeling ◽  
Productive Phase ◽  
The Impact ◽  
New Algorithms

We reassess progress in the field of biomolecular modeling and simulation, following up on our perspective published in 2011. By reviewing metrics for the field's productivity and providing examples of success, we underscore the productive phase of the field, whose short-term expectations were overestimated and long-term effects underestimated. Such successes include prediction of structures and mechanisms; generation of new insights into biomolecular activity; and thriving collaborations between modeling and experimentation, including experiments driven by modeling. We also discuss the impact of field exercises and web games on the field's progress. Overall, we note tremendous success by the biomolecular modeling community in utilization of computer power; improvement in force fields; and development and application of new algorithms, notably machine learning and artificial intelligence. The combined advances are enhancing the accuracy and scope of modeling and simulation, establishing an exemplary discipline where experiment and theory or simulations are full partners. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Nutritional Preconditioning in Cancer Treatment in Relation to DNA Damage and Aging

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Winnie M.C. van den Boogaard ◽  
Marry M. van den Heuvel-Eibrink ◽  
Jan H.J. Hoeijmakers ◽  
Wilbert P. Vermeij
Keyword(s):  
Dna Damage ◽  
Cancer Treatment ◽  
Cancer Biology ◽  
Accelerated Aging ◽  
Nutritional Intervention ◽  
Annual Review ◽  
Publication Date ◽  
Short And Long Term ◽  
Resilience Mechanisms

Dietary restriction (DR) is the most successful nutritional intervention for extending life span and preserving health in numerous species. Reducing food intake triggers a protective response that shifts energy resources from growth to maintenance and resilience mechanisms. This so-called survival response has been shown to particularly increase life and health span and decrease DNA damage in DNA repair–deficient mice exhibiting accelerated aging. Accumulation of DNA damage is the main cause of aging, but also of cancer. Moreover, radiotherapies and most chemotherapies are based on damaging DNA, consistent with their ability to induce toxicity and accelerate aging. Since fasting and DR decrease DNA damage and its effects, nutritional preconditioning holds promise for improving (cancer) therapy and preventing short- and long-term side effects of anticancer treatments. This review provides an overview of the link between aging and cancer, highlights important preclinical studies applying such nutritional preconditioning, and summarizes the first clinical trials implementing nutritional preconditioning in cancer treatment. Expected final online publication date for the Annual Review of Cancer Biology, Volume 5 is March 4, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Adaptation

2016 ◽  
Author(s):  
Andrew P. Hendry
Keyword(s):  
Genetic Variation ◽  
Adaptive Evolution ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Phenotypic Change ◽  
Adaptive Landscapes ◽  
Local Environments ◽  
Short And Long Term ◽  
Different Populations

This chapter outlines how to conceptualize and predict adaptive evolution based on information about selection and genetic variation. It introduces and explains adaptive landscapes, a concept that has proven useful in guiding the understanding of evolution. The chapter also reviews empirical data to answer fundamental questions about adaptation in nature, including to what extent short- and long-term evolution is predictable, how fast is phenotypic change, to what extent is adaptation constrained by genetic variation, and how well adapted natural populations are to their local environments. Moving beyond selection and adaptation within populations, the chapter shows how eco-evolutionary dynamics will be shaped by biological diversity: that is, different populations and species have different effects on their environment.

Cardiovascular Effects of Particulate Air Pollution

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Aruni Bhatnagar
Keyword(s):  
Fossil Fuels ◽  
Fine Particulate Matter ◽  
Cardiovascular Effects ◽  
Premature Mortality ◽  
Annual Review ◽  
Publication Date ◽  
Particulate Air Pollution ◽  
Underlying Mechanisms ◽  
Disease Exposure

Inhalation of fine particulate matter (PM2.5), produced by the combustion of fossil fuels, is an important risk factor for cardiovascular disease. Exposure to PM2.5 has been linked to increases in blood pressure, thrombosis, and insulin resistance. It also induces vascular injury and accelerates atherogenesis. Results from animal models corroborate epidemiological evidence and suggest that the cardiovascular effects of PM2.5 may be attributable, in part, to oxidative stress, inflammation, and the activation of the autonomic nervous system. Although the underlying mechanisms remain unclear, there is robust evidence that long-term exposure to PM2.5 is associated with premature mortality due to heart failure, stoke, and ischemic heart disease. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

Science ◽  
2018 ◽  
Vol 360 (6395) ◽  
pp. 1355-1358 ◽  
Author(s):  
Matthew R. Jones ◽  
L. Scott Mills ◽  
Paulo Célio Alves ◽  
Colin M. Callahan ◽  
Joel M. Alves ◽  
...  
Keyword(s):  
Genetic Variants ◽  
High Frequency ◽  
Coat Color ◽  
Ecological Traits ◽  
Interspecific Gene Flow ◽  
Mild Winter ◽  
Adaptive Introgression ◽  
Changing Environments ◽  
Snowshoe Hares ◽  
History Of

Snowshoe hares (Lepus americanus) maintain seasonal camouflage by molting to a white winter coat, but some hares remain brown during the winter in regions with low snow cover. We show that cis-regulatory variation controlling seasonal expression of the Agouti gene underlies this adaptive winter camouflage polymorphism. Genetic variation at Agouti clustered by winter coat color across multiple hare and jackrabbit species, revealing a history of recurrent interspecific gene flow. Brown winter coats in snowshoe hares likely originated from an introgressed black-tailed jackrabbit allele that has swept to high frequency in mild winter environments. These discoveries show that introgression of genetic variants that underlie key ecological traits can seed past and ongoing adaptation to rapidly changing environments.

Gut Microbiota in Intestinal and Liver Disease

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Rheinallt M. Jones ◽  
Andrew S. Neish
Keyword(s):  
Community Structure ◽  
Liver Disease ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Alimentary Tract ◽  
Annual Review ◽  
Publication Date ◽  
Proinflammatory Gene ◽  
Gene Regulatory

It is known that the gut microbiota, the numerically vast and taxonomically diverse microbial communities that thrive in a symbiotic fashion within our alimentary tract, can affect the normal physiology of the gastrointestinal tract and liver. Further, disturbances of the microbiota community structure from both endogenous and exogenous influences as well as the failure of host responsive mechanisms have been implicated in a variety of disease processes. Mechanistically, alterations in intestinal permeability and dysbiosis of the microbiota can result in inflammation, immune activation, and exposure to xenobiotic influences. Additionally, the gut and liver are continually exposed to small molecule products of the microbiota with proinflammatory, gene regulatory, and oxidative properties. Long-term coevolution has led to tolerance and incorporation of these influences into normal physiology and homeostasis; conversely, changes in this equilibrium from either the host or the microbial side can result in a wide variety of immune, inflammatory, metabolic, and neoplastic intestinal and hepatic disorders. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 16 is January 25, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genetics of Thoroughbred Racehorse Performance

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Ernest Bailey ◽  
Jessica L. Petersen ◽  
Theodore S. Kalbfleisch
Keyword(s):  
Genetic Variation ◽  
Annual Review ◽  
Publication Date ◽  
The Past ◽  
Racing Performance ◽  
Thoroughbred Horses ◽  
Genomic Tools ◽  
Dna Variants ◽  
Different Types ◽  
Genomic Regions

Thoroughbred horses have been selected for racing performance for more than 400 years. Despite continued selection, race times have not improved significantly during the past 60 years, raising the question of whether genetic variation for racing performance still exists. Studies using phenotypes such as race time, money earned, and handicapping, however, demonstrate that there is extensive variation within these traits and that they are heritable. Even so, these are poor measures of racing success since Thoroughbreds race at different ages and distances and on different types of tracks, and some may not race at all. With the advent of genomic tools, DNA variants are being identified that contribute to racing success. Aside from strong associations for myostatin variants with best racing distance, weak to modest associations with racing phenotypes are reported for other genomic regions. These data suggest that diverse genetic strategies have contributed to producing a successful racehorse, and genetic variation contributing to athleticism remains important. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Role of Community Science in Entomology

2021 ◽  
Vol 67 (1) ◽  
Author(s):  
Mary M. Gardiner ◽  
Helen E. Roy
Keyword(s):  
Large Scale ◽  
Annual Review ◽  
Publication Date ◽  
Data Sets ◽  
Pest Monitoring ◽  
The Status ◽  
Control Community ◽  
Patterns And Processes ◽  
Community Science

Community (or citizen) science, the involvement of volunteers in scientific endeavors, has a long history. Over the past few centuries, the contributions of volunteers to our understanding of patterns and processes in entomology has been inspiring. From the collation of large-scale and long-term data sets, which have been instrumental in underpinning our knowledge of the status and trends of many insect groups, to action, including species management, whether for conservation or control, community scientists have played pivotal roles. Contributions, such as pest monitoring by farmers and species discoveries by amateur naturalists, set foundations for the research engaging entomologists today. The next decades will undoubtedly bring new approaches, tools, and technologies to underpin community science. The potential to increase inclusion within community science is providing exciting opportunities within entomology. An increase in the diversity of community scientists, alongside increasing taxonomic and geographic breadth of initiatives, will bring enormous benefits globally for people and nature. Expected final online publication date for the Annual Review of Entomology, Volume 67 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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