In Brief |
Featured
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Opinion |
Revising the human mutation rate: implications for understanding human evolution
Recent measurements of the human mutation rate using next-generation sequencing have revealed a value of approximately half of that previously derived from fossil calibration. Here, the authors discuss the implications of this revised mutation rate in relation to our understanding of human evolution.
- Aylwyn Scally
- & Richard Durbin
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Review Article |
Harnessing genomics and genome biology to understand malaria biology
This Review describes how genome-wide analyses have provided various insights into the most lethal malarial parasite,Plasmodium falciparum, including determinants of antimalarial drug resistance. The authors also propose how genetic tools can be refined to monitor future therapeutic interventions.
- Sarah K. Volkman
- , Daniel E. Neafsey
- & Dyann F. Wirth
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Review Article |
Molecular phylogenetics: principles and practice
Phylogenetic analysis is pervading every field of biological study. The authors review and assess the main methods of phylogenetic analysis — including parsimony, distance, likelihood and Bayesian methods — and provide guidance for selecting the most appropriate approach and software package.
- Ziheng Yang
- & Bruce Rannala
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Reply |
Universal pleiotropy is not a valid null hypothesis: reply to Hill and Zhang
- Günter P. Wagner
- & Jianzhi Zhang
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Correspondence |
Assessing pleiotropy and its evolutionary consequences: pleiotropy is not necessarily limited, nor need it hinder the evolution of complexity
- William G. Hill
- & Xu-Sheng Zhang
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Review Article |
Rare and common variants: twenty arguments
This Review presents arguments for and against each of two main models for the genetic basis of complex traits. It concludes that the infinitesimal model is essentially correct, but that rare, large-effect alleles also make an essential contribution to disease risk.
- Greg Gibson
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Reply |
Response to 'Familial risks in understanding type 1 diabetes genetics'
- Constantin Polychronakos
- & Quan Li
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Review Article |
Computer simulations: tools for population and evolutionary genetics
Computer simulations can be valuable components of studies in many fields, including population genetics, evolutionary biology, genetic epidemiology and ecology. The recent increase in the available range of software packages is now making simulation an accessible option for researchers with limited bioinformatics experience.
- Sean Hoban
- , Giorgio Bertorelle
- & Oscar E. Gaggiotti
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Review Article |
Crop genomics: advances and applications
The increased availability of reference genomes and the ability to obtain resequencing data in larger quantities are changing the capabilities of crop comparative genomics. Insights into the genetic basis of domestication and agriculturally important traits are emerging, and improved genomic tools have implications for crop breeders and evolutionary biologists.
- Peter L. Morrell
- , Edward S. Buckler
- & Jeffrey Ross-Ibarra
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Review Article |
Genetic contributions to behavioural diversity at the gene–environment interface
The authors review our understanding of how common genetic variation contributes to behavioural diversity, explaining how these variants modulate an organism's interaction with the environment and defining gene classes — such as those affecting sensory or neuromodulatory pathways — that are preferentially associated with behavioural variation.
- Andres Bendesky
- & Cornelia I. Bargmann
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Review Article |
Molecular spandrels: tests of adaptation at the genetic level
Although many studies claim to have detected an adaptive allele, this label is not always applied rigorously. The authors argue that obtaining direct evidence that specific alleles are adaptive requires approaches which functionally connect genotype, phenotype and fitness.
- Rowan D. H. Barrett
- & Hopi E. Hoekstra
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Review Article |
Variation in the mutation rate across mammalian genomes
Large genomic data sets are revealing that mutation rates vary across genomes at many different scales, from the effects caused by neighbouring nucleotides to patterns that affect whole chromosomes. These varying mutation rates have implications for inherited and somatic disease.
- Alan Hodgkinson
- & Adam Eyre-Walker
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Review Article |
Haplotype phasing: existing methods and new developments
The authors review the experimental and computational approaches for determining haplotype phase, focusing on statistical methods, the factors that influence the strategy used and the value of using information on identity-by-descent.
- Sharon R. Browning
- & Brian L. Browning
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Review Article |
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
The recent surge in sequencing output has uncovered a wealth of genetic variation, but interpretation of these data remains a challenge. This Review discusses computational and experimental methods for estimating the deleteriousness and functional significance of genetic variants to better identify those that are potentially causal for disease.
- Gregory M. Cooper
- & Jay Shendure
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Review Article |
Learning about human population history from ancient and modern genomes
Next-generation sequencing has now been used to produce the first ancient hominin genome sequences and is also being used to sequence modern humans from many different populations. Together with SNP genotyping, these data are transforming views of human history.
- Mark Stoneking
- & Johannes Krause
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Viewpoint |
The future of model organisms in human disease research
The genetic architecture of human disease is often hard to replicate in model organisms, and disease modelling in human cells is rapidly improving. Six leading model organism researchers provide their perspective on where this leaves non-human models of disease.
- Timothy J. Aitman
- , Charles Boone
- & Derek L. Stemple
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Progress |
New approaches to disease mapping in admixed populations
The increased genetic diversity in populations with recent ancestry from more than one continent may help in the identification of genetic variants underlying disease risk. This Progress article discusses recent developments in methods to study complex traits in these admixed populations, including combining SNP and admixture association signals.
- Michael F. Seldin
- , Bogdan Pasaniuc
- & Alkes L. Price
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Review Article |
Genome-wide genetic marker discovery and genotyping using next-generation sequencing
The authors describe the best practices for a growing number of methods that use next-generation sequencing to rapidly discover and assess genetic markers across any genome, with applications from population genomics and quantitative trait locus mapping to marker-assisted selection.
- John W. Davey
- , Paul A. Hohenlohe
- & Mark L. Blaxter
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Review Article |
Family-based designs for genome-wide association studies
Linkage studies have identified the genetic basis of several Mendelian disorders, but in recent years this method has been superseded by association mapping. The unique advantages of linkage studies support the combined use of linkage and association designs for identifying new genetic variants related to human traits.
- Jurg Ott
- , Yoichiro Kamatani
- & Mark Lathrop
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Review Article |
Using electronic health records to drive discovery in disease genomics
Increasing efforts are being made to integrate electronic health records into disease genetics and genomics studies and to use the biological 'by-products' of health-care for research. Such efforts promise to decrease the cost of genomics studies and increase their clinical relevance.
- Isaac S. Kohane
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Review Article |
Genotype and SNP calling from next-generation sequencing data
An overview of the steps required in converting next-generation sequencing (NGS) data into accurate called SNPs and genotypes, a process that is crucial for the many downstream analyses of NGS data.
- Rasmus Nielsen
- , Joshua S. Paul
- & Yun S. Song
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Correspondence |
Tests of association for rare variants: case control mutation screening
- Sean V. Tavtigian
- , Mia Hashibe
- & Alun Thomas
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Comment |
Adaptation – not by sweeps alone
There has been recent progress in identifying selective sweeps underlying a range of adaptations. Jonathan Pritchard and Anna Di Rienzo argue that many adaptive events in natural populations may occur by polygenic adaptation, which would largely go undetected by conventional methods for detecting selection.
- Jonathan K. Pritchard
- & Anna Di Rienzo
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Review Article |
Measuring selection in contemporary human populations
Are humans evolving? Applying evolutionary biology tools to large-scale medical and epidemiological data sets shows that traits in many human populations are experiencing natural selection and have the genetic potential to respond to it.
- Stephen C. Stearns
- , Sean G. Byars
- & Douglas Ewbank
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Correspondence |
Missing heritability in genome-wide association study research
- Paolo Vineis
- & Neil Pearce
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Progress |
New approaches to population stratification in genome-wide association studies
This article compares the different approaches that have been developed for detecting confounding due to population stratification, family structure and cryptic relatedness, with an emphasis on the potential of mixed models for addressing these problems simultaneously.
- Alkes L. Price
- , Noah A. Zaitlen
- & Nick Patterson
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Review Article |
The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts
The authors discuss the evolutionary dynamics of antibiotic resistance in bacteria in relation to the complex interplay between population genetic factors and the spatial and temporal pattern of antibiotic use.
- R. Craig MacLean
- , Alex R. Hall
- & Angus Buckling
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Review Article |
Genome-wide association studies in diverse populations
Most genome-wide association (GWA) studies have been performed in populations of European descent. This Review discusses the substantial potential and the challenges of extending consideration of GWA studies to diverse worldwide populations.
- Noah A. Rosenberg
- , Lucy Huang
- & Michael Boehnke
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Review Article |
How culture shaped the human genome: bringing genetics and the human sciences together
Theoretical, anthropological and genetic studies suggest that human evolution has been shaped by gene–culture interactions. This Review collates data from these diverse fields, and highlights the potential for cross-disciplinary exchange to provide novel insights into how culture has shaped the human genome.
- Kevin N. Laland
- , John Odling-Smee
- & Sean Myles
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Review Article |
Methodological challenges of genome-wide association analysis in Africa
Genome-wide association studies are not widespread in Africa, partly because of the challenges of dealing with population structure and high genomic diversity. New approaches in statistical imputation and whole-genome sequencing are now set to exploit these features for fine mapping causal variants.
- Yik-Ying Teo
- , Kerrin S. Small
- & Dominic P. Kwiatkowski
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