Literature DB >> 26553329

Methods and models for unravelling human evolutionary history.

Joshua G Schraiber1, Joshua M Akey1.   

Abstract

The genomes of contemporary humans contain considerable information about the history of our species. Although the general contours of human evolutionary history have been defined with increasing resolution throughout the past several decades, the continuing deluge of massively large sequencing data sets presents new opportunities and challenges for understanding human evolutionary history. Here, we review the signatures that demographic history imparts on patterns of DNA sequence variation, statistical methods that have been developed to leverage information contained in genome-scale data sets and insights gleaned from these studies. We also discuss the importance of using exploratory analyses to assess data quality, the strengths and limitations of commonly used population genomics methods, and factors that confound population genomics inferences.

Entities:  

Mesh:

Year:  2015        PMID: 26553329     DOI: 10.1038/nrg4005

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  118 in total

1.  Directional selection and the site-frequency spectrum.

Authors:  C D Bustamante; J Wakeley; S Sawyer; D L Hartl
Journal:  Genetics       Date:  2001-12       Impact factor: 4.562

2.  Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.

Authors:  Na Li; Matthew Stephens
Journal:  Genetics       Date:  2003-12       Impact factor: 4.562

3.  Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.

Authors:  Bruce Rannala; Ziheng Yang
Journal:  Genetics       Date:  2003-08       Impact factor: 4.562

4.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Authors:  Heng Li; Jue Ruan; Richard Durbin
Journal:  Genome Res       Date:  2008-08-19       Impact factor: 9.043

Review 5.  Positive natural selection in the human lineage.

Authors:  P C Sabeti; S F Schaffner; B Fry; J Lohmueller; P Varilly; O Shamovsky; A Palma; T S Mikkelsen; D Altshuler; E S Lander
Journal:  Science       Date:  2006-06-16       Impact factor: 47.728

6.  Genome-wide inference of ancestral recombination graphs.

Authors:  Matthew D Rasmussen; Melissa J Hubisz; Ilan Gronau; Adam Siepel
Journal:  PLoS Genet       Date:  2014-05-15       Impact factor: 5.917

7.  Inference of human population history from individual whole-genome sequences.

Authors:  Heng Li; Richard Durbin
Journal:  Nature       Date:  2011-07-13       Impact factor: 49.962

8.  Forces shaping the fastest evolving regions in the human genome.

Authors:  Katherine S Pollard; Sofie R Salama; Bryan King; Andrew D Kern; Tim Dreszer; Sol Katzman; Adam Siepel; Jakob S Pedersen; Gill Bejerano; Robert Baertsch; Kate R Rosenbloom; Jim Kent; David Haussler
Journal:  PLoS Genet       Date:  2006-08-23       Impact factor: 5.917

9.  ANGSD: Analysis of Next Generation Sequencing Data.

Authors:  Thorfinn Sand Korneliussen; Anders Albrechtsen; Rasmus Nielsen
Journal:  BMC Bioinformatics       Date:  2014-11-25       Impact factor: 3.169

10.  Estimating selection coefficients in spatially structured populations from time series data of allele frequencies.

Authors:  Iain Mathieson; Gil McVean
Journal:  Genetics       Date:  2013-01-10       Impact factor: 4.562

View more
  41 in total

1.  Patterns of deleterious variation between human populations reveal an unbalanced load.

Authors:  Rajiv C McCoy; Joshua M Akey
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-19       Impact factor: 11.205

2.  Admixture, Population Structure, and F-Statistics.

Authors:  Benjamin M Peter
Journal:  Genetics       Date:  2016-02-08       Impact factor: 4.562

3.  Modeling Human Population Separation History Using Physically Phased Genomes.

Authors:  Shiya Song; Elzbieta Sliwerska; Sarah Emery; Jeffrey M Kidd
Journal:  Genetics       Date:  2016-11-09       Impact factor: 4.562

4.  Inferring Identical-by-Descent Sharing of Sample Ancestors Promotes High-Resolution Relative Detection.

Authors:  Monica D Ramstetter; Sushila A Shenoy; Thomas D Dyer; Donna M Lehman; Joanne E Curran; Ravindranath Duggirala; John Blangero; Jason G Mezey; Amy L Williams
Journal:  Am J Hum Genet       Date:  2018-06-21       Impact factor: 11.025

5.  Howling from the past: historical phylogeography and diversity losses in European grey wolves.

Authors:  Christophe Dufresnes; Christian Miquel; Nadège Remollino; François Biollaz; Nicolas Salamin; Pierre Taberlet; Luca Fumagalli
Journal:  Proc Biol Sci       Date:  2018-08-01       Impact factor: 5.349

6.  Bayesian Analysis of Evolutionary Divergence with Genomic Data under Diverse Demographic Models.

Authors:  Yujin Chung; Jody Hey
Journal:  Mol Biol Evol       Date:  2017-06-01       Impact factor: 16.240

Review 7.  Explosive genetic evidence for explosive human population growth.

Authors:  Feng Gao; Alon Keinan
Journal:  Curr Opin Genet Dev       Date:  2016-10-04       Impact factor: 5.578

Review 8.  Recent advances in the study of fine-scale population structure in humans.

Authors:  John Novembre; Benjamin M Peter
Journal:  Curr Opin Genet Dev       Date:  2016-09-20       Impact factor: 5.578

9.  GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data.

Authors:  Ekaterina Noskova; Vladimir Ulyantsev; Klaus-Peter Koepfli; Stephen J O'Brien; Pavel Dobrynin
Journal:  Gigascience       Date:  2020-03-01       Impact factor: 6.524

10.  Nonparametric coalescent inference of mutation spectrum history and demography.

Authors:  William S DeWitt; Kameron Decker Harris; Aaron P Ragsdale; Kelley Harris
Journal:  Proc Natl Acad Sci U S A       Date:  2021-05-25       Impact factor: 11.205

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.