Oly Genetics 104, NF GenePop Analysis
Tried to do the html to .md trick for this notebook, but it did not function. No biggie, since there are no pretty plots in this notebook. Original notebooks: R markdown version, NF-GenePop-Analysis.Rmd; HTML version, NF-GenePop-Analysis.html
In this notebook I will use the GenePop R program to analyze the 2016/2017 Fidalgo Bay (NF) Ostrea lurida microsatellite data; the results from each analysis are housed in a series of .txt files.
Prior to importing the data, prepared the 2016/2017 NF data in Excel and exported into GenePop format; resulting file is available on 2018-01-22-Preparing-for-Genepop.md
First, install GenePop program;
install.packages("genepop")
library(genepop)
Pull basic information on allele and genotype frequencies per locus and per sample
basic_info(inputFile="Data/Oly2016NFH+2017NFW_Merged.txt", outputFile = "Analyses/NF-Basic-Info.txt", verbose=T)
Resulting file: “NF-Basic-Info.txt” Hetero- and homozygosity info pasted here:
NF Wild
| Loci | Olur10 | Olur11 | Olur12 | Olur13 | Olur15 | Olur19 |
|---|---|---|---|---|---|---|
| Expected Homozygotes | 4.99 | 24.59 | 11.83 | 6.68 | 6.66 | 6.64 |
| Observed Homozygotes | 2 | 28 | 12 | 7 | 6 | 7 |
| Expected Heterozygotes | 92.01 | 70.41 | 86.17 | 91.32 | 91.34 | 90.36 |
| Observed Heterozygotes | 95 | 67 | 86 | 91 | 92 | 90 |
NF Hatchery
| Loci | Olur10 | Olur11 | Olur12 | Olur13 | Olur15 | Olur19 |
|---|---|---|---|---|---|---|
| Expected Homozygotes | 5.02 | 23.03 | 13.44 | 7.14 | 7.22 | 7.10 |
| Observed Homozygotes | 7 | 27 | 5 | 6 | 6 | 7 |
| Expected Heterozygotes | 92.98 | 70.97 | 86.56 | 88.86 | 90.78 | 88.90 |
| Observed Heterozygotes | 91 | 67 | 95 | 90 | 92 | 89 |
Assess whether loci are in Hardy-Weinberg Equilibrium
test_HW(inputFile = "Data/Oly2016NFH+2017NFW_Merged.txt", which="Proba", outputFile = "Analyses/NF-HWE.txt", enumeration = FALSE, dememorization = 10000, batches = 500, iterations = 2000, verbose = interactive())
Resulting file: “NF-HWE.txt” All P-values across loci in each population are »0.05, do not reject the null hypothesis that all loci are in HWE.
Pop : NFW-2017
-----------------------------------------
Fis estimates
---------------
locus P-val S.E. W&C R&H Steps
----------- ------- ------- ------- ------- ------
Olur10 0.2885 0.0155 -0.0327 -0.0097 22774 switches
Olur11 0.7817 0.0096 0.0487 0.0823 32358 switches
Olur12 0.9079 0.0055 0.0020 -0.0093 77677 switches
Olur13 0.3355 0.0108 0.0035 0.0086 83321 switches
Olur15 0.3031 0.0111 -0.0073 -0.0015 68376 switches
Olur19 0.3528 0.0109 0.0040 0.0092 82550 switches
All (Fisher's method):
Chi2 : 9.8276
Df : 12.0000
Prob : 0.6311
Pop : NFH-2016
-----------------------------------------
Fis estimates
---------------
locus P-val S.E. W&C R&H Steps
----------- ------- ------- ------- ------- ------
Olur10 0.6622 0.0165 0.0214 0.0184 19734 switches
Olur11 0.7706 0.0105 0.0563 0.0169 29904 switches
Olur12 0.8312 0.0070 -0.0981 -0.0520 86460 switches
Olur13 0.1129 0.0057 -0.0129 -0.0057 112034 switches
Olur15 0.0795 0.0057 -0.0135 -0.0123 93919 switches
Olur19 0.1101 0.0065 -0.0012 0.0012 89921 switches
All (Fisher's method):
Chi2 : 15.5530
Df : 12.0000
Prob : 0.2126
==========================================
All locus, all populations
==========================================
All (Fisher's method) :
Chi2 : 25.3806
Df : 24.0000
Prob : 0.3853
Assess whether any loci are linked
test_LD(inputFile = "Data/Oly2016NFH+2017NFW_Merged.txt", outputFile = "Analyses/NF-LD.txt", dememorization = 10000, batches = 100, iterations = 1000, verbose = TRUE)
Resulting file: “NF-LD.txt” Interesting, results from this Linkage Disequilibrium test indicate that there are, in fact, linked loci:
Pop Locus#1 Locus#2 P-Value S.E. Switches
---------- ------- ------- -------- -------- --------
NFW-2017 Olur10 Olur11 0.32418 0.045606 216
NFW-2017 Olur10 Olur12 0.372000 0.048411 65
NFW-2017 Olur11 Olur12 1.000000 0.000000 435
NFW-2017 Olur10 Olur13 1.000000 0.000000 42
NFW-2017 Olur11 Olur13 0.990730 0.006526 279
NFW-2017 Olur12 Olur13 0.144450 0.034977 90
NFW-2017 Olur10 Olur15 1.000000 0.000000 33
NFW-2017 Olur11 Olur15 0.975760 0.014058 232
NFW-2017 Olur12 Olur15 1.000000 0.000000 96
NFW-2017 Olur13 Olur15 0.065770 0.024413 35
NFW-2017 Olur10 Olur19 1.000000 0.000000 35
NFW-2017 Olur11 Olur19 1.000000 0.000000 229
NFW-2017 Olur12 Olur19 1.000000 0.000000 91
NFW-2017 Olur13 Olur19 0.060010 0.023868 16
NFW-2017 Olur15 Olur19 0.000000 0.000000 28 <------ Wild 15 & 19 linked
NFH-2016 Olur10 Olur11 1.000000 0.000000 154
NFH-2016 Olur10 Olur12 0.208400 0.040527 72
NFH-2016 Olur11 Olur12 0.923220 0.024857 520
NFH-2016 Olur10 Olur13 1.000000 0.000000 45
NFH-2016 Olur11 Olur13 0.726700 0.043512 284
NFH-2016 Olur12 Olur13 0.000000 0.000000 151 <------ Hatchery 12 & 13 linked
NFH-2016 Olur10 Olur15 1.000000 0.000000 36
NFH-2016 Olur11 Olur15 0.715690 0.043815 301
NFH-2016 Olur12 Olur15 0.049120 0.021532 165
NFH-2016 Olur13 Olur15 0.000000 0.000000 68 <------ Hatchery 13 & 15 linked
NFH-2016 Olur10 Olur19 1.000000 0.000000 40
NFH-2016 Olur11 Olur19 0.716270 0.042213 282
NFH-2016 Olur12 Olur19 0.000000 0.000000 149 <------ Hatchery 12 & 19 linked
NFH-2016 Olur13 Olur19 0.000000 0.000000 54 <------ Hatchery 13 & 19 linked
NFH-2016 Olur15 Olur19 0.000000 0.000000 44 <------ Hatchery 15 & 19 linked
P-value for each locus pair across all populations
(Fisher's method)
-----------------------------------------------------
Locus pair Chi2 df P-Value
-------------------- -------- --- --------
Olur10 & Olur11 2.252913 4 0.689355
Olur10 & Olur12 5.114315 4 0.275768
Olur11 & Olur12 0.159775 4 0.996974
Olur10 & Olur13 0.000000 4 1.000000
Olur11 & Olur13 0.657110 4 0.956511
Olur12 & Olur13 >35.7544134 <0.000000 <------ 12 & 13 linked
Olur10 & Olur15 0.000000 4 1.000000
Olur11 & Olur15 0.718094 4 0.949079
Olur12 & Olur15 6.026978 4 0.197143
Olur13 & Olur15 >37.3279524 <0.000000 <------ 13 & 15 linked
Olur10 & Olur19 0.000000 4 1.000000
Olur11 & Olur19 0.667396 4 0.955288
Olur12 & Olur19 >31.8847694 <0.000002 <------ 12 & 19 linked
Olur13 & Olur19 >37.5112584 <0.000000 <------ 13 & 19 linked
Olur15 & Olur19 >63.7695394 <0.000000 <------ 15 & 19 linked
Assess for null alleles
nulls(inputFile = "Data/Oly2016NFH+2017NFW_Merged.txt", outputFile = "Analyses/NF-null.txt", nullAlleleMethod = "B96", CIcoverage = 0.95, verbose = TRUE)
Resulting file: “NF-null.txt” Null allele frequences low; will compare with results from MicroChecker to confirm.
(Locus by population) table of estimated null allele frequencies
================================================================
Locus: Populations (! names truncated to 6 characters):
NFW-20 NFH-20
-----------------------------------------------------
Olur10 0.0000 0.0079
Olur11 0.0125 0.0159
Olur12 0.0000 0.0000
Olur13 0.0000 0.0000
Olur15 0.0000 0.0000
Olur19 0.0000 0.0000
================================================================
Confidence intervals for null allele frequencies
=================================================
Frequency 0.0250 0.9750
Locus Population estimate bound bound
-------------------------------------------------
Olur10 NFW-2017 0.0000 (No info for CI)
NFH-2016 0.0079 0.0000 0.0422
Olur11 NFW-2017 0.0125 0.0000 0.0694
NFH-2016 0.0159 0.0000 0.0724
Olur12 NFW-2017 0.0000 (No info for CI)
NFH-2016 0.0000 (No info for CI)
Olur13 NFW-2017 0.0000 (No info for CI)
NFH-2016 0.0000 (No info for CI)
Olur15 NFW-2017 0.0000 (No info for CI)
NFH-2016 0.0000 (No info for CI)
Olur19 NFW-2017 0.0000 (No info for CI)
NFH-2016 0.0000 (No info for CI)
=================================================
Exact conditional contingency-table test or genotypic differentiation.
Assesses the distribution of diploid genotypes in the various populations. The null hypothesis tested is Ho: “genotypes are drawn from the same distribution in all populations”
test_diff(inputFile = "Data/Oly2016NFH+2017NFW_Merged.txt", outputFile = "Analyses/NF-Diff.txt", genic=FALSE, pairs=TRUE, dememorization = 10000, batches = 100, iterations = 1000, verbose = TRUE)
Resulting file: “NF-Diff.txt” Results indicate that genotypes are drawn from the same distribution, as P».01 for all loci.
Locus Population pair P-Value S.E. Switches
----------- --------------------- ------- ------- --------
Olur10 NFH-2016 & NFW-2017 0.32784 0.01552 27018
Olur11 NFH-2016 & NFW-2017 0.54191 0.01155 36148
Olur12 NFH-2016 & NFW-2017 0.67662 0.01140 38491
Olur13 NFH-2016 & NFW-2017 0.08560 0.00745 32174
Olur15 NFH-2016 & NFW-2017 0.06505 0.00713 32414
Olur19 NFH-2016 & NFW-2017 0.15165 0.01146 32502
P-value for each population pair across all loci
(Fisher's method)
-----------------------------------------------------
Population pair Chi2 df P-Value
-------------------- -------- --- --------
NFW-2017 & NFH-2016 18.39076 12 0.104331
Calculate Fst for each population
Fst is a measure of genetic structure (developed by Sewall Wright, 1969, 1978), and is related to statistical analysis of variance (ANOVA). FST is the proportion of the total genetic variance contained in a subpopulation (the S subscript) relative to the total genetic variance (the T subscript). Values can range from 0 to 1. High FST implies a considerable degree of differentiation among populations.
Fst(inputFile = "Data/Oly2016NFH+2017NFW_Merged.txt", outputFile = "Analyses/NF-Fst.txt", sizes=F, pairs=TRUE, dataType="Diploid", verbose = TRUE)
Resulting file: “NF-Fst.txt” Values are very close to zero, which indicates that there is little genetic differentiation among wild and hatchery populations.
Indices for populations:
---- -------------
1 NFW-2017
2 NFH-2016
----------------------
Estimates for each locus:
========================
Locus: Olur10
---------------------------------
pop 1
2 -0.0007
Locus: Olur11
---------------------------------
pop 1
2 -0.0027
Locus: Olur12
---------------------------------
pop 1
2 -0.0020
Locus: Olur13
---------------------------------
pop 1
2 0.0030
Locus: Olur15
---------------------------------
pop 1
2 0.0036
Locus: Olur19
---------------------------------
pop 1
2 0.0027
Estimates for all loci (diploid):
=========================
pop 1
2 0.0008
Generate stats on allelic diversity. Interpretation TBD.
genedivFis(inputFile="Data/Oly2016NFH+2017NFW_Merged.txt", sizes=FALSE, outputFile = "Analyses/NF-DivFis.txt", dataType = "Diploid", verbose=interactive())
Resulting file: “NF-DivFis.txt”
Written on January 22, 2018