期刊论文详细信息
BMC Bioinformatics
Haplotype based testing for a better understanding of the selective architecture
Research
Marta Pelizzola1  Andreas Futschik2  Haoyu Chen3 
[1] Aarhus University, Aarhus, Denmark;Johannes Kepler University of Linz, Linz, Austria;University of Veterinary Medicine Vienna, Vienna, Austria;Vienna Graduate School of Population Genetics, Vienna, Austria;
关键词: Hypothesis test;    Post hoc test;    Selection;    Evolve and resequence;    Experimental evolution;    Haplotype;   
DOI  :  10.1186/s12859-023-05437-3
 received in 2022-11-29, accepted in 2023-08-03,  发布年份 2023
来源: Springer
PDF
【 摘 要 】

BackgroundThe identification of genomic regions affected by selection is one of the most important goals in population genetics. If temporal data are available, allele frequency changes at SNP positions are often used for this purpose. Here we provide a new testing approach that uses haplotype frequencies instead of allele frequencies.ResultsUsing simulated data, we show that compared to SNP based test, our approach has higher power, especially when the number of candidate haplotypes is small or moderate. To improve power when the number of haplotypes is large, we investigate methods to combine them with a moderate number of haplotype subsets. Haplotype frequencies can often be recovered with less noise than SNP frequencies, especially under pool sequencing, giving our test an additional advantage. Furthermore, spurious outlier SNPs may lead to false positives, a problem usually not encountered when working with haplotypes. Post hoc tests for the number of selected haplotypes and for differences between their selection coefficients are also provided for a better understanding of the underlying selection dynamics. An application on a real data set further illustrates the performance benefits.ConclusionsDue to less multiple testing correction and noise reduction, haplotype based testing is able to outperform SNP based tests in terms of power in most scenarios.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

【 预 览 】
附件列表
Files Size Format View
RO202309157037279ZK.pdf 3217KB PDF download
Fig. 10 467KB Image download
Fig. 1 146KB Image download
Fig. 5 144KB Image download
Fig. 1 293KB Image download
MediaObjects/12888_2023_5022_MOESM2_ESM.docx 106KB Other download
42490_2023_74_Article_IEq35.gif 1KB Image download
13068_2023_2361_Article_IEq1.gif 1KB Image download
Fig. 5 728KB Image download
Fig. 2 738KB Image download
MediaObjects/12888_2023_5079_MOESM1_ESM.tiff 3100KB Other download
13690_2023_1154_Article_IEq6.gif 1KB Image download
13690_2023_1154_Article_IEq7.gif 1KB Image download
13690_2023_1154_Article_IEq8.gif 1KB Image download
13690_2023_1154_Article_IEq17.gif 1KB Image download
Table 2 271KB Table download
40517_2023_261_Article_IEq31.gif 1KB Image download
Fig. 3 251KB Image download
MediaObjects/12974_2023_2861_MOESM2_ESM.tif 30484KB Other download
Fig. 4 226KB Image download
MediaObjects/12888_2023_5086_MOESM3_ESM.docx 575KB Other download
MediaObjects/42004_2023_986_MOESM6_ESM.docx 12133KB Other download
12888_2023_5113_Article_IEq1.gif 1KB Image download
Fig. 3 715KB Image download
Fig. 3 415KB Image download
Fig. 1 424KB Image download
Fig. 1 159KB Image download
12862_2023_2133_Article_IEq10.gif 1KB Image download
Fig. 3 676KB Image download
Fig. 2 646KB Image download
Fig. 3 511KB Image download
Fig. 7 721KB Image download
Fig. 2 99KB Image download
Fig. 1 349KB Image download
Fig. 3 2436KB Image download
MediaObjects/12888_2023_5081_MOESM3_ESM.xls 221KB Other download
Fig. 2 238KB Image download
Fig. 1 1174KB Image download
Fig. 2 478KB Image download
Fig. 2 813KB Image download
Fig. 2 198KB Image download
Fig. 1 80KB Image download
MediaObjects/12951_2023_1994_MOESM2_ESM.pdf 555KB PDF download
Fig. 1 1128KB Image download
Fig. 1 761KB Image download
MediaObjects/12974_2023_2855_MOESM6_ESM.tif 36752KB Other download
Fig. 3 404KB Image download
Fig. 2 73KB Image download
MediaObjects/41408_2023_892_MOESM9_ESM.xlsx 6057KB Other download
Fig. 3 118KB Image download
Fig. 6 632KB Image download
Fig. 1 1164KB Image download
Fig. 2 216KB Image download
Fig. 2 53KB Image download
Fig. 1 2029KB Image download
Fig. 6 4041KB Image download
Fig. 4 263KB Image download
Fig. 3 335KB Image download
12862_2023_2133_Article_IEq130.gif 1KB Image download
Fig. 2 68KB Image download
Fig. 3 321KB Image download
Fig. 4 42KB Image download
Fig. 3 162KB Image download
Fig. 5 44KB Image download
Fig. 4 1411KB Image download
MediaObjects/12888_2023_5047_MOESM1_ESM.docx 26KB Other download
Fig. 2 151KB Image download
MediaObjects/12888_2023_5047_MOESM2_ESM.docx 19KB Other download
MediaObjects/12974_2023_2873_MOESM3_ESM.tif 1195KB Other download
1520KB Image download
Fig. 2 72KB Image download
Fig. 1 322KB Image download
MediaObjects/12888_2023_4955_MOESM1_ESM.docx 12KB Other download
Fig. 2 165KB Image download
Fig. 3 368KB Image download
Fig. 2 373KB Image download
Fig. 6 634KB Image download
Fig. 3 232KB Image download
Fig. 7 2382KB Image download
Fig. 8 593KB Image download
Fig. 7 1396KB Image download
Fig. 4 141KB Image download
Fig. 3 121KB Image download
Fig. 2 563KB Image download
Fig. 5 86KB Image download
Fig. 11 1966KB Image download
Fig. 1 538KB Image download
MediaObjects/40560_2023_680_MOESM1_ESM.docx 144KB Other download
40517_2023_266_Article_IEq52.gif 1KB Image download
40517_2023_266_Article_IEq56.gif 1KB Image download
MediaObjects/12947_2023_311_MOESM4_ESM.docx 81KB Other download
MediaObjects/12951_2023_1985_MOESM3_ESM.pdf 1543KB PDF download
Fig. 2 1138KB Image download
Fig. 2 227KB Image download
Fig. 1 99KB Image download
MediaObjects/42004_2023_979_MOESM3_ESM.pdf 20727KB PDF download
Fig. 6 737KB Image download
Fig. 1 592KB Image download
13690_2023_1151_Article_IEq1.gif 1KB Image download
910KB Image download
40854_2023_507_Article_IEq31.gif 1KB Image download
Scheme 1 960KB Image download
Fig. 1 75KB Image download
Fig. 2 262KB Image download
Fig. 2 79KB Image download
MediaObjects/41016_2023_334_MOESM1_ESM.docx 1997KB Other download
Fig. 5 1259KB Image download
40798_2023_599_Article_IEq18.gif 1KB Image download
Fig. 11 2958KB Image download
40798_2023_599_Article_IEq20.gif 1KB Image download
Fig. 3 429KB Image download
Fig. 3 386KB Image download
40798_2023_599_Article_IEq23.gif 1KB Image download
41512_2023_153_Article_IEq65.gif 1KB Image download
Fig. 3 353KB Image download
MediaObjects/12974_2023_2872_MOESM3_ESM.docx 3368KB Other download
Fig. 5 655KB Image download
Fig. 1 1703KB Image download
Fig. 2 154KB Image download
Fig. 3 497KB Image download
MediaObjects/12888_2023_5043_MOESM1_ESM.docx 49KB Other download
MediaObjects/12864_2023_9600_MOESM10_ESM.pdf 264KB PDF download
Fig. 6 368KB Image download
MediaObjects/12951_2023_2012_MOESM7_ESM.jpg 1995KB Other download
MediaObjects/40798_2023_616_MOESM1_ESM.docx 5055KB Other download
MediaObjects/12951_2023_2028_MOESM1_ESM.docx 5703KB Other download
41512_2023_153_Article_IEq93.gif 1KB Image download
MediaObjects/12944_2023_1889_MOESM1_ESM.zip 1350KB Package download
MediaObjects/13063_2023_7442_MOESM1_ESM.docx 29KB Other download
MediaObjects/40249_2023_1127_MOESM1_ESM.docx 2825KB Other download
Fig. 4 1902KB Image download
Fig. 2 223KB Image download
Fig. 1 205KB Image download
MediaObjects/13690_2023_1137_MOESM1_ESM.docx 55KB Other download
Fig. 1 317KB Image download
41512_2023_153_Article_IEq101.gif 1KB Image download
41512_2023_153_Article_IEq102.gif 1KB Image download
Fig. 3 286KB Image download
Fig. 1 305KB Image download
Fig. 3 2026KB Image download
Fig. 7 580KB Image download
MediaObjects/12951_2023_2012_MOESM8_ESM.jpg 5545KB Other download
MediaObjects/40345_2023_307_MOESM1_ESM.docx 2857KB Other download
Fig. 1 73KB Image download
Fig. 1 272KB Image download
Fig. 8 2696KB Image download
Fig. 5 2153KB Image download
Fig. 3 45KB Image download
MediaObjects/41021_2023_275_MOESM1_ESM.pdf 408KB PDF download
Fig. 2 922KB Image download
Fig. 2 88KB Image download
40517_2023_267_Article_IEq3.gif 1KB Image download
40517_2023_267_Article_IEq4.gif 1KB Image download
40517_2023_267_Article_IEq6.gif 1KB Image download
MediaObjects/12974_2023_2871_MOESM1_ESM.tif 19056KB Other download
Fig. 1 273KB Image download
MediaObjects/13046_2021_2137_MOESM4_ESM.tif 8416KB Other download
Fig. 3 477KB Image download
Fig. 3 367KB Image download
Fig. 1 490KB Image download
Fig. 2 957KB Image download
41512_2023_153_Article_IEq116.gif 1KB Image download
MediaObjects/41021_2023_275_MOESM2_ESM.pdf 466KB PDF download
Fig. 2 437KB Image download
MediaObjects/40249_2023_1127_MOESM2_ESM.xlsx 31KB Other download
Fig. 9 5258KB Image download
Fig. 5 374KB Image download
40798_2023_622_Article_IEq4.gif 1KB Image download
MediaObjects/41021_2023_275_MOESM3_ESM.pdf 408KB PDF download
40798_2023_622_Article_IEq6.gif 2KB Image download
Fig. 1 227KB Image download
【 图 表 】

Fig. 1

40798_2023_622_Article_IEq6.gif

40798_2023_622_Article_IEq4.gif

Fig. 5

Fig. 9

Fig. 2

41512_2023_153_Article_IEq116.gif

Fig. 2

Fig. 1

Fig. 3

Fig. 3

Fig. 1

40517_2023_267_Article_IEq6.gif

40517_2023_267_Article_IEq4.gif

40517_2023_267_Article_IEq3.gif

Fig. 2

Fig. 2

Fig. 3

Fig. 5

Fig. 8

Fig. 1

Fig. 1

Fig. 7

Fig. 3

Fig. 1

Fig. 3

41512_2023_153_Article_IEq102.gif

41512_2023_153_Article_IEq101.gif

Fig. 1

Fig. 1

Fig. 2

Fig. 4

41512_2023_153_Article_IEq93.gif

Fig. 6

Fig. 3

Fig. 2

Fig. 1

Fig. 5

Fig. 3

41512_2023_153_Article_IEq65.gif

40798_2023_599_Article_IEq23.gif

Fig. 3

Fig. 3

40798_2023_599_Article_IEq20.gif

Fig. 11

40798_2023_599_Article_IEq18.gif

Fig. 5

Fig. 2

Fig. 2

Fig. 1

Scheme 1

40854_2023_507_Article_IEq31.gif

13690_2023_1151_Article_IEq1.gif

Fig. 1

Fig. 6

Fig. 1

Fig. 2

Fig. 2

40517_2023_266_Article_IEq56.gif

40517_2023_266_Article_IEq52.gif

Fig. 1

Fig. 11

Fig. 5

Fig. 2

Fig. 3

Fig. 4

Fig. 7

Fig. 8

Fig. 7

Fig. 3

Fig. 6

Fig. 2

Fig. 3

Fig. 2

Fig. 1

Fig. 2

Fig. 2

Fig. 4

Fig. 5

Fig. 3

Fig. 4

Fig. 3

Fig. 2

12862_2023_2133_Article_IEq130.gif

Fig. 3

Fig. 4

Fig. 6

Fig. 1

Fig. 2

Fig. 2

Fig. 1

Fig. 6

Fig. 3

Fig. 2

Fig. 3

Fig. 1

Fig. 1

Fig. 1

Fig. 2

Fig. 2

Fig. 2

Fig. 1

Fig. 2

Fig. 3

Fig. 1

Fig. 2

Fig. 7

Fig. 3

Fig. 2

Fig. 3

12862_2023_2133_Article_IEq10.gif

Fig. 1

Fig. 1

Fig. 3

Fig. 3

12888_2023_5113_Article_IEq1.gif

Fig. 4

Fig. 3

40517_2023_261_Article_IEq31.gif

13690_2023_1154_Article_IEq17.gif

13690_2023_1154_Article_IEq8.gif

13690_2023_1154_Article_IEq7.gif

13690_2023_1154_Article_IEq6.gif

Fig. 2

Fig. 5

13068_2023_2361_Article_IEq1.gif

42490_2023_74_Article_IEq35.gif

Fig. 1

Fig. 5

Fig. 1

Fig. 10

【 参考文献 】
  • [1]
  • [2]
  • [3]
  • [4]
  • [5]
  • [6]
  • [7]
  • [8]
  • [9]
  • [10]
  • [11]
  • [12]
  • [13]
  • [14]
  • [15]
  • [16]
  • [17]
  • [18]
  • [19]
  • [20]
  • [21]
  • [22]
  • [23]
  • [24]
  • [25]
  • [26]
  • [27]
  • [28]
  • [29]
  • [30]
  • [31]
  • [32]
  • [33]
  • [34]
  • [35]
  • [36]
  • [37]
  • [38]
  • [39]
  • [40]
  • [41]
  • [42]
  • [43]
  • [44]
  文献评价指标  
  下载次数:5次 浏览次数:0次