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Eukaryote Genomes [chapter]

Naruya Saitou
2013 Introduction to Evolutionary Genomics  
It will be interesting to examine genome sizes of species related to the Perigord black truffl e, so as to infer the evolutionary period when the genome size expansion occurred.  ...  From the initial stage of molecular evolutionary studies, protein noncoding regions were suspected to be involved in gene regulation (Zuckerkandl and Pauling 1965; Britten and Davidson 1971; King and Wilson  ... 
doi:10.1007/978-1-4471-5304-7_8 fatcat:egkplrndkjafhfvjqwzkhoyyra

Neutral Evolution [chapter]

Naruya Saitou
2013 Introduction to Evolutionary Genomics  
Neutral evolution is the default process of the genome changes. This is because our world is finite and the randomness is important when we consider history of a finite world.  ...  Expected evolutionary patterns under neutrality are then discussed on fixation probability, rate of evolution, and amount of DNA variation kept in population.  ...  Because the majority of eukaryotic genome is evolving in this fashion, the understanding of the pure neutral evolutionary process is quite important for evolutionary genomics.  ... 
doi:10.1007/978-1-4471-5304-7_4 fatcat:x47wb7pxbvhnbob5ettvkpviwa

Evolutionary Puzzles: An Introduction to Genome Rearrangement [chapter]

Mathieu Blanchette
2001 Lecture Notes in Computer Science  
This paper is intended to serve as an introduction to genome rearrangement and its use for inferring phylogenetic trees.  ...  We then consider the problem of inferring phylogenetic (evolutionary) trees from genetic data. We briefly present the two major approaches to solve this problem.  ...  Gene arrangement can also be used to infer evolutionary relationships among species.  ... 
doi:10.1007/3-540-45718-6_106 fatcat:4gmsmubsmfbitfryfdmrhmw42y

Introduction to evolutionary genomic approaches to human disease

Louis J. Muglia, Dhavendra Kumar
2013 Applied and Translational Genomics  
Introduction to evolutionary genomic approaches to human disease ☆ This special edition of Applied & Translational Genomics, "Evolutionary Genomic Approaches to Human Disease", provides 6 articles that  ...  The reviews and new analytic papers comprising this special edition reflect the power incorporating evolutionary influences the genomic, developmental and physiological studies hold.  ... 
doi:10.1016/j.atg.2013.10.003 pmid:27896053 pmcid:PMC5121262 fatcat:cl35vipzgja4jkawwcdbg3i4ba

Extracting Evolutionary Insights Using Bioinformatics

Dmitry Sherbakov, Yuri Panchin, Ancha Baranova
2013 International Journal of Genomics  
and to comparative genomics of cancer-specific genes.  ...  We should not forget that evolutionary genomics is still an emerging field in biology.  ... 
doi:10.1155/2013/376235 pmid:24324950 pmcid:PMC3845244 fatcat:wc75n52rcza3fmzqjabov46tfq

Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions

Rafael Dudeque Zenni, Ian A. Dickie, Michael J. Wingfield, Heidi Hirsch, Casparus J. Crous, Laura A. Meyerson, Treena I. Burgess, Thalita G. Zimmermann, Metha M. Klock, Evan Siemann, Alexandra Erfmeier, Roxana Aragon (+2 others)
2016 AoB Plants  
Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success.  ...  The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-byenvironment interactions, admixture, hybridization, polyploidization, rapid  ...  Introduction Evolutionary processes are important mechanisms contributing to successful biological invasions.  ... 
doi:10.1093/aobpla/plw085 pmid:28039118 pmcid:PMC5391705 fatcat:ef6lozy6yjb2raiwrnve7oxxey

Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016–2017

Gilberto A. Santiago, Chaney C. Kalinich, Fabiola Cruz-López, Glenda L. González, Betzabel Flores, Aaron Hentoff, Keyla N. Charriez, Joseph R. Fauver, Laura E. Adams, Tyler M. Sharp, Allison Black, Trevor Bedford (+6 others)
2021 Emerging Infectious Diseases  
We reconstructed the 2016-2017 Zika virus epidemic in Puerto Rico by using complete genomes to uncover the epidemic's origin, spread, and evolutionary dynamics.  ...  Our study revealed that the epidemic was propelled by multiple introductions that spread across the island, intricate evolutionary patterns, and ≈10 months of cryptic transmission.  ...  virus epidemic in Puerto Rico by using complete genomes to uncover the epidemic's origin, spread, and evolutionary dynamics.  ... 
doi:10.3201/eid2711.211575 pmid:34670646 pmcid:PMC8544999 fatcat:6znmlczplfdfrc6hlus4elg6xa

The Logic of Evolution: Review of the Logic of Chance by Eugene V. Koonin

Richard D. Emes
2012 Frontiers in Genetics  
From Darwin and the central messages of the "origin of species" through an excellent introduction to the modern synthesis of the mid twentieth century to the "genomics revolution" of the latter twentieth  ...  By comparison to the world of physics, the methods and theory of comparative genomics and evolutionary biology are used to investigate the possibilities of universals in evolution.  ... 
doi:10.3389/fgene.2012.00135 fatcat:r3o6qcjtwza2jcpatpkunifdnm

GeneTRACE-reconstruction of gene content of ancestral species

V. Kunin, C. A. Ouzounis
2003 Bioinformatics  
In this paper, we describe GENETRACE, an efficient linear-time algorithm that allows the reconstruction of evolutionary history of individual protein families as well as the complete gene content of ancestral  ...  SimulEv simulations were also used to evaluate performance of the reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate at the terminal branches but suffer  ...  Acknowledgements We thank members of the Computational Genomics Group for discussions. This work was supported by the European Molecular Biology Laboratory. C.  ... 
doi:10.1093/bioinformatics/btg174 pmid:12874054 fatcat:m6msjfqc5netjhdhkwk2jnb6ha

Page 215 of Biological Reviews Vol. 88, Issue 1 [page]

2013 Biological Reviews  
To date, only a few Amoebozoa genomes have been sequenced completely, for several species that represent some of the major evolutionary lineages in this clade.  ...  CONTENTS Introduction (1) Comparative genomics (2) Phylogeny of Amoebozoa Nuclear genomes in amoebozoa 1) General genomic features (2) Archamoebae (3) Acanthamoebidae (4) Myxogastria (5) Dictyostelida  ... 

Ecology, Evolution, and the Genome: A "Whole-Elephant" Reader's Guide

2004 BioScience  
Cullis begins with an introduction to what has been discovered so far about the structure and organization of plant genomes.  ...  If ecological and evolutionary genomics is to emerge as a fullfledged field of investigation, then genomic approaches will need to be brought to bear on the broad range of ecological and evolutionary questions  ... 
doi:10.1641/0006-3568(2004)054[0950:eeatga];2 fatcat:jgdvetivb5ailpq46r27fxbhdu

Introduction to the special issue: Tree invasions: towards a better understanding of their complex evolutionary dynamics

Heidi Hirsch, David M. Richardson, Johannes J. Le Roux
2017 AoB Plants  
The papers cover a wide range of evolutionary mechanisms in tree genomes (adaptation), epigenomes (phenotypic plasticity) and their second genomes (mutualists), and show how such mechanisms can impact  ...  The collection of papers in this issue has helped to identify and assess the evolutionary mechanisms that are likely to influence tree invasions.  ...  Thanks are also due to the Editor-in-Chief and editorial staff of AoB PLANTS for their support during the completion of this Special Issue.  ... 
doi:10.1093/aobpla/plx014 pmid:28533897 pmcid:PMC5420828 fatcat:lbnrf26yi5adjhwo664fzntsve

Evolutionary Mechanisms of Microbial Genomes 2012

Hiromi Nishida, Shinji Kondo, Hideaki Nojiri, Ken-ichi Noma, Kenro Oshima
2012 International Journal of Evolutionary Biology  
Two papers are presented on subjects related to evolution of base composition in genomes. H.  ...  The special issue "Evolutionary mechanisms of microbial genomes" has been launched in 2011 and presented 11 original papers.  ...  In closing this introduction to the special issue, we would like to express our full appreciation to all the authors and reviewers for their enormous efforts that have made the timely completion of our  ... 
doi:10.1155/2012/872768 pmid:22957300 pmcid:PMC3432360 fatcat:2hsltjvjorhltniscukwinnnue

Insights from Population Genomics to Enhance and Sustain Biological Control of Insect Pests

Arun Sethuraman, Fredric J. Janzen, David W. Weisrock, John J. Obrycki
2020 Insects  
Recent advances in genomic sequencing technology and model-based statistical methods to analyze population-scale genomic data provide a much needed impetus for biological control programs to benefit by  ...  incorporating a consideration of evolutionary consequences.  ...  Category Ecological Parameters Evolutionary Parameters Genomic Method Evolutionary Perspective Non-target effects, invasiveness Other species, other than target/pests Selection, demography  ... 
doi:10.3390/insects11080462 pmid:32708047 pmcid:PMC7469154 fatcat:rg7r2d7ckzdkpdjk46e3quaegm

Analytical approaches to genomic evolution

D. Sankoff
1993 Biochimie  
We model the non-local mechanisms of genomic evolution and propose methods for studying the evolutionary divergence of species based on these models.  ...  Each of these is studied in the context of a different type of genomic data. We introduce the theory of phylogenetic invanants for evolutionary inference based on very long macromolecular sequences.  ...  Genomic comparison, as an approach to inferring evolutionary divergence, must take account of all these processes.  ... 
doi:10.1016/0300-9084(93)90174-q pmid:8347727 fatcat:czaxnxyzingybp5lbrdd4mns5u
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