Detecting natural selection in genomic data

JJ Vitti, SR Grossman, PC Sabeti - Annual review of genetics, 2013 - annualreviews.org
The past fifty years have seen the development and application of numerous statistical
methods to identify genomic regions that appear to be shaped by natural selection. These …

Population genomics of rapid adaptation by soft selective sweeps

PW Messer, DA Petrov - Trends in ecology & evolution, 2013 - cell.com
Organisms can often adapt surprisingly quickly to evolutionary challenges, such as the
application of pesticides or antibiotics, suggesting an abundant supply of adaptive genetic …

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

M Li, S Tian, L Jin, G Zhou, Y Li, Y Zhang, T Wang… - Nature …, 2013 - nature.com
We report the sequencing at 131× coverage, de novo assembly and analyses of the genome
of a female Tibetan wild boar. We also resequenced the whole genomes of 30 Tibetan wild …

Robust identification of local adaptation from allele frequencies

T Günther, G Coop - Genetics, 2013 - academic.oup.com
Comparing allele frequencies among populations that differ in environment has long been a
tool for detecting loci involved in local adaptation. However, such analyses are complicated …

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

Q Long, FA Rabanal, D Meng, CD Huber, A Farlow… - Nature …, 2013 - nature.com
Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic
variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from …

[HTML][HTML] Identifying recent adaptations in large-scale genomic data

SR Grossman, KG Andersen, I Shlyakhter, S Tabrizi… - Cell, 2013 - cell.com
Although several hundred regions of the human genome harbor signals of positive natural
selection, few of the relevant adaptive traits and variants have been elucidated. Using full …

Detecting signatures of selection through haplotype differentiation among hierarchically structured populations

MI Fariello, S Boitard, H Naya, M SanCristobal… - Genetics, 2013 - academic.oup.com
The detection of molecular signatures of selection is one of the major concerns of modern
population genetics. A widely used strategy in this context is to compare samples from …

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

S Zhao, P Zheng, S Dong, X Zhan, QI Wu, X Guo… - Nature Genetics, 2013 - nature.com
The panda lineage dates back to the late Miocene and ultimately leads to only one extant
species, the giant panda (Ailuropoda melanoleuca). Although global climate change and …

Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data

TS Korneliussen, I Moltke, A Albrechtsen, R Nielsen - BMC bioinformatics, 2013 - Springer
Background A number of different statistics are used for detecting natural selection using
DNA sequencing data, including statistics that are summaries of the frequency spectrum …

A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry

KL Monda, GK Chen, KC Taylor, C Palmer… - Nature …, 2013 - nature.com
Genome-wide association studies (GWAS) have identified 36 loci associated with body
mass index (BMI), predominantly in populations of European ancestry. We conducted a …