Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments.
adaptation
allele frequencies
coverage
evolve-and-resequence
haplotypes
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
03 12 2019
03 12 2019
Historique:
pubmed:
23
10
2019
medline:
21
4
2020
entrez:
23
10
2019
Statut:
epublish
Résumé
Evolve-and-resequence (E+R) experiments leverage next-generation sequencing technology to track the allele frequency dynamics of populations as they evolve. While previous work has shown that adaptive alleles can be detected by comparing frequency trajectories from many replicate populations, this power comes at the expense of high-coverage (>100x) sequencing of many pooled samples, which can be cost-prohibitive. Here, we show that accurate estimates of allele frequencies can be achieved with very shallow sequencing depths (<5x) via inference of known founder haplotypes in small genomic windows. This technique can be used to efficiently estimate frequencies for any number of bi-allelic SNPs in populations of any model organism founded with sequenced homozygous strains. Using both experimentally-pooled and simulated samples of
Identifiants
pubmed: 31636085
pii: g3.119.400755
doi: 10.1534/g3.119.400755
pmc: PMC6893198
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
4159-4168Subventions
Organisme : NIGMS NIH HHS
ID : F32 GM097837
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM100366
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM118165
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG000044
Pays : United States
Informations de copyright
Copyright © 2019 Tilk et al.
Références
Bioinformatics. 2014 Feb 15;30(4):576-7
pubmed: 24336146
Mol Biol Evol. 2012 Apr;29(4):1187-97
pubmed: 22114362
Mol Biol Evol. 2017 Jan;34(1):174-184
pubmed: 27702776
Nature. 2010 Sep 30;467(7315):587-90
pubmed: 20844486
Mol Biol Evol. 2014 Dec;31(12):3228-39
pubmed: 25172959
Mol Biol Evol. 2014 Feb;31(2):474-83
pubmed: 24214537
Nat Genet. 2012 Sep;44(9):1015-9
pubmed: 22902787
G3 (Bethesda). 2014 Jul 01;4(9):1657-65
pubmed: 24989146
PLoS One. 2015 Oct 13;10(10):e0140462
pubmed: 26461136
Bioinformatics. 2009 Dec 15;25(24):3296-302
pubmed: 19861356
PLoS One. 2015 May 22;10(5):e0128036
pubmed: 26000737
Proc Biol Sci. 2018 Jan 10;285(1870):
pubmed: 29321302
Bioinformatics. 2015 Feb 15;31(4):515-22
pubmed: 25304780
Heredity (Edinb). 2015 May;114(5):431-40
pubmed: 25269380
Genetics. 2015 Apr;199(4):991-1005
pubmed: 25672748
PLoS Genet. 2012;8(10):e1002905
pubmed: 23071443
Mol Biol Evol. 2015 Oct;32(10):2616-32
pubmed: 26044351
Genome Res. 2014 Jul;24(7):1193-208
pubmed: 24714809
Science. 1999 Jul 16;285(5426):422-4
pubmed: 10411508
Nucleic Acids Res. 2017 Jan 4;45(D1):D650-D657
pubmed: 27701074
Science. 2010 Oct 15;330(6002):376-9
pubmed: 20947767
Mol Biol Evol. 2013 May;30(5):1145-58
pubmed: 23364324
Genome Biol. 2015 Oct 01;16:219
pubmed: 26438066
PLoS One. 2012;7(7):e41901
pubmed: 22848651
Mol Biol Evol. 2016 Dec;33(12):3308-3313
pubmed: 27687565
Genome Biol Evol. 2014 Apr 30;6(5):1210-8
pubmed: 24787620
PLoS One. 2011 Jan 05;6(1):e15292
pubmed: 21264334
Mol Biol Evol. 2014 Apr;31(4):1040-55
pubmed: 24441104
Nat Rev Genet. 2015 Oct;16(10):567-82
pubmed: 26347030
Genetics. 2011 Jan;187(1):245-60
pubmed: 21059887
G3 (Bethesda). 2017 Jul 5;7(7):2337-2343
pubmed: 28546383
Ecol Evol. 2016 Aug 30;6(20):7169-7175
pubmed: 27895897
PLoS One. 2012;7(11):e48588
pubmed: 23152785
Nat Genet. 2009 Feb;41(2):251-7
pubmed: 19136954
Proc Biol Sci. 2012 Dec 22;279(1749):5029-38
pubmed: 22833271
Nature. 2009 Oct 29;461(7268):1243-7
pubmed: 19838166
Mol Ecol. 2012 Oct;21(20):4931-41
pubmed: 22726122
Genetics. 2012 Jun;191(2):633-42
pubmed: 22466043
BMC Bioinformatics. 2016 Mar 11;17:125
pubmed: 26968756
BMC Bioinformatics. 2013 Sep 08;14:270
pubmed: 24010487
Mol Biol Evol. 2017 Apr 01;34(4):831-842
pubmed: 28087779