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SUPPLEMENTARY MATERIAL
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METHODS AND RESULTS OF A TEST FOR GENOME-WIDE WEAK TRANSMISSION
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DISTORTION IN FAVOUR OF MAJOR ALLELES.
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METHODS
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Aparicio et al. (2010) suggested that weak transmission distortion may more
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commonly favor the major alleles due to recessive deleterious mutations, which are
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more likely to be associated with the minor alleles (though founder effects in our
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population are expected to add noise to this relationship). To get an estimate of the
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genome-wide transmission ratio of the major allele, we first sampled one SNP from
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each chromosome, then summed up all inheritance events of the major and minor
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alleles of these SNPs and calculated the transmission ratio. We repeated this 10,000
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times and calculated the 95% quantile range (QR).
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RESULTS
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Summing up the informative inheritance events did not show a consistent
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transmission bias in favor of the major alleles across all loci (combined-sexes
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transmission ratio [95% QR] = 0.501 [0.493–0.509], female-specific transmission
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ratio = 0.501 [0.493–0.510], male-specific transmission ratio = 0.501 [0.492–0.511]).
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DISCUSSION
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Neither in the combined-sexes nor in the sex-specific genome scans did we detect
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any sign of weak genome-wide transmission bias. A small effect in favor of major
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alleles may be expected due to recessive deleterious mutations, which are more
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likely to be associated with the minor alleles and which was found by Aparicio et al.
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(2010) in a wild population of lesser kestrels. However, those minor alleles that are
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indeed linked to recessive deleterious mutations may be at especially low
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frequencies and their effect would be masked by SNPs with higher allele frequencies
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(which are more likely not linked to recessive deleterious mutations) and founder
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effects could additionally change allele frequencies in captivity. Also, a weak
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transmission bias towards major alleles might be expected if genotyping errors were
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common (Mitchell et al. 2003). In any case, major and minor alleles were inherited
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with similar probabilities in our population.
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Although examples for segregation distorters are sparse and probably prone to
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detection bias, classical distorters often bias transmission by more than 90% (Lyttle
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1993) and often have low stable equilibrium frequencies in a population (e.g.
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Presgraves et al. 2009). We found 12 and 17 segregating haplotypes on
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chromosomes Tgu2 and Tgu5, respectively, and a previous study identified 17
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haplotypes across the ESR1 gene on chromosome Tgu3 (Forstmeier et al. 2012),
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which suggests that we were unable to tag all low frequency haplotypes within our
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population with a unique marker since on average we had 39 SNPs per chromosome
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(median 27 SNPs). However, more than 79% of the SNPs would detect transmission
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rates of 0.7 with 80% power, such that transmission distortion of SNPs which tag
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multiple non-driving haplotypes along with the driving haplotype could be detected.
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Nonetheless, in the genome-wide scans we did not identify any such strong
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distorters but they could potentially be still present at low frequency or on the eight
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chromosomes missing in the current genome assembly (Pigozzi & Solari 1998;
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Warren et al. 2010).
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Studies on transmission distortion in other bird species were based on comparable
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numbers of informative meioses as our initial scan and also showed only subtle
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departures from Mendelian segregation (Aparicio et al. 2010; Axelsson et al. 2010).
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Since their results were not replicated in independent sets of birds, conclusions
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should be treated carefully, as illustrated by our data on chromosome Tgu5. In a
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recent paper, Ellegren et al. (2012) suggested to test for meiotic drive by extensive
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genotyping in pedigrees because they found genomic divergence peaks between
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two flycatcher species close to potential centromeres and telomeres and invoke a
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meiotic drive model of speciation. Such studies could easily be conducted with
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microsatellite markers used for paternity analysis in wild populations, although
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genome-wide coverage is difficult to achieve. However, as replication is the gold
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standard for validation of any genetic association study (NCI-NHGRI Working Group
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on Replication in Association Studies 2007), following guidelines for replication
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should also be crucial when testing for transmission distortion.
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REFERENCES
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Aparicio JM, Ortego J, Calabuig G, Cordero PJ (2010) Evidence of subtle departures
from Mendelian segregation in a wild lesser kestrel (Falco naumanni)
population. Heredity 105, 213–219.
Axelsson E, Albrechtsen A, Van AP, et al. (2010) Segregation distortion in chicken
and the evolutionary consequences of female meiotic drive in birds. Heredity
105, 290–298.
Ellegren H, Smeds L, Burri R, et al. (2012) The genomic landscape of species
divergence in Ficedula flycatchers. Nature 491, 756–760.
Forstmeier W, Schielzeth H, Mueller JC, Ellegren H, Kempenaers B (2012)
Heterozygosity-fitness correlations in zebra finches: microsatellite markers
can be better than their reputation. Molecular Ecology 21, 3237–3249.
Lyttle TW (1993) Cheaters sometimes prosper: distortion of mendelian segregation
by meiotic drive. Trends in Genetics 9, 205–210.
Mitchell AA, Cutler DJ, Chakravarti A (2003) Undetected genotyping errors cause
apparent overtransmission of common alleles in the
transmission/disequilibrium test. American Journal of Human Genetics 72,
598–610.
NCI-NHGRI Working Group on Replication in Association Studies, Chanock SJ,
Manolio T, et al. (2007) Replicating genotype-phenotype associations. Nature
447, 655–660.
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Pigozzi MI, Solari AJ (1998) Germ cell restriction and regular transmission of an
accessory chromosome that mimics a sex body in the zebra finch,
Taeniopygia guttata. Chromosome Research 6, 105–113.
Presgraves DC, Gerard PR, Cherukuri A, Lyttle TW (2009) Large-scale selective
sweep among segregation distorter chromosomes in African populations of
Drosophila melanogaster. Plos Genetics 5, e1000463.
Warren WC, Clayton DF, Ellegren H, et al. (2010) The genome of a songbird. Nature
464, 757–762.
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FIGURES
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Figure S1: (A) Histogram of the number of informative meioses available for each SNP in the initial
whole genome scans. For the sex-specific scans we here exclude all cases where both parents are
heterozygous. (B) Power analysis for the number of informative meioses for different transmission
ratios considering a P-value of 4.0 x 10-5 as significant.
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108
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Figure S2: Whole-genome transmission ratios in (A) both heterozygous sexes
combined, (B) heterozygous female parents only and (C) heterozygous male parents
only. On the abscissa are the chromosomes and on the ordinate are transmission
ratios of the major allele for each SNP. The dashed line indicates fair segregation of
0.5. Chromosome TguZ was tested only in males because only males carry two
copies of TguZ. Those SNPs with transmission ratios above 0.8 or below 0.2 had
less than 10 informative meioses.
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Figure S3: Whole-genome scans for transmission distortion in (A) heterozygous
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female parents only, excluding those pairs in which both female and male are
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heterozygous and (B) heterozygous male parents only, excluding those pairs in
114
which both male and female are heterozygous. On the abscissa are the
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chromosomes and on the ordinate are the -log10(P-values). The dashed line
116
indicates the significance threshold after genome-wide Bonferroni correction and the
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dotted line before genome-wide Bonferroni correction. Chromosome TguZ was
118
tested only in males because only males carry two copies of TguZ.
119
Table S1: Primer sequences, positions in the genome and melting temperatures used in the PCR.
Microsatellite
Start
End
Tgu5_SD
35,669,252
35,669,308
Tgu5_SD4
Tgu2_SD44
Tgu2_SD60
38,137,613
43,803,808
60,167,999
38,137,648
43,803,904
60,168,042
Distance
to SNP
(Mb)
2.15
0.32
19.01
35.37
Motif
Primer
name
Sequence
Tm
(°C)
TG
-F
CTACAGTCAGTGAAACCGTTC
57
-R
GCATGGAACTGCATGCCTTA
57
CA
TG
CA
-F
CCCTTGGGGCTTCTCATCAT
58
-R
TGCACCATCCCACTGAACTG
58
-F
TGGAAGTGGCAAGGACAACA
57
-R
TCCCTGCTCCCTATCTGTAT
57
-F
CGTCCCAAAACACCAATCGT
57
-R
CCTCACAACACGAAGCAGAT
57
120
Table S2: Transmission ratio of locus rs82439270 on chromosome Tgu5 in the
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follow-up analysis for both heterozygous males and females separately. The follow-
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up analysis consisted of (1) a replicate of the initial genome-wide scan which
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contained only birds that hatched (survived), (2) embryos that died naturally during
124
incubation (died embryos) and (3) embryos that were collected for DNA analysis
125
before hatching or whose egg shells broke and whose fate is thus unknown (other
126
embryos). The observed number of inheritance events of the major allele is shown
127
under nA.
Informative
Sex
Sample
Transmission
nA
meioses
females
P-value
survived
640
311
0.486
0.447, 0.525
0.50
died embryos
245
123
0.502
0.438, 0.566
1.00
other embryos
422
223
0.528
0.480, 0.577
0.26
1307
657
0.503
0.475, 0.530
0.87
survived
679
332
0.489
0.451, 0.527
0.59
died embryos
220
109
0.495
0.428, 0.563
0.95
other embryos
338
186
0.55
0.496, 0.604
0.073
1237
627
0.507
0.479, 0.535
0.65
all
males
95% CI
ratio
all
128
Table S3: Summary of all transmission ratios for the driving locus on chromosome
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Tgu2 in heterozygous females + both parents heterozygous, males + both parents
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heterozygous, combined sexes, only heterozygous females (excluding cases where
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both parents are heterozygous) and only heterozygous males (excluding cases
132
where both parents are heterozygous). The observed number of inheritance events
133
of the major allele is shown under nA.
Informative
Sex
Sample
Transmission
nA
meioses
females
males
combined
95% CI
P-value
ratio
genome scan
106
76
0.717
0.621, 0.800
9 x 10-6
follow-up 1 survived
121
59
0.488
0.396, 0.580
0.86
follow-up 1 died embryos
60
33
0.55
0.416, 0.679
0.52
follow-up 1 other embryos
109
64
0.587
0.489, 0.681
0.084
follow-up 1 all
290
156
0.538
0.479, 0.596
0.22
follow-up 2 all
262
146
0.557
0.495, 0.618
0.073
all
658
378
0.574
0.536, 0.613
0.00015
genome scan
90
53
0.589
0.480, 0.692
0.11
follow-up 1 survived
85
48
0.565
0.453, 0.672
0.28
follow-up 1 died embryos
42
24
0.571
0.410, 0.723
0.44
follow-up 1 other embryos
92
55
0.598
0.490, 0.699
0.076
follow-up 1 all
219
127
0.58
0.512, 0.646
0.021
follow-up 2 all
232
132
0.569
0.503, 0.634
0.042
all
541
312
0.577
0.534, 0.619
0.00041
genome scan
160
103
0.644
0.564, 0.718
0.00034
follow-up 1 survived
178
94
0.528
0.452, 0.603
0.50
follow-up 1 died embryos
90
52
0.578
0.469, 0.681
0.17
follow-up 1 other embryos
179
106
0.592
0.516, 0.665
0.017
follow-up 1 all
447
252
0.564
0.516, 0.610
0.0080
follow-up 2 all
494
278
0.563
0.518, 0.607
0.0060
1101
633
0.575
0.545, 0.604
7 x 10-7
all
10
females only
males only
genome scan
70
50
0.714
0.594, 0.816
0.00044
follow-up 1 survived
93
46
0.495
0.389, 0.600
1.00
follow-up 1 died embryos
48
28
0.583
0.432, 0.724
0.31
follow-up 1 other embryos
87
51
0.586
0.476, 0.691
0.13
follow-up 1 all
228
125
0.548
0.481, 0.614
0.16
follow-up 2 all
262
146
0.557
0.495, 0.618
0.073
all
560
321
0.573
0.531, 0.615
0.00061
genome scan
54
27
0.5
0.361, 0.639
1.00
follow-up 1 survived
57
35
0.614
0.476, 0.740
0.11
follow-up 1 died embryos
30
19
0.633
0.439, 0.801
0.20
follow-up 1 other embryos
70
42
0.6
0.476, 0.715
0.12
follow-up 1 all
157
96
0.611
0.531, 0.688
0.0065
follow-up 2 all
232
132
0.569
0.503, 0.634
0.042
all
443
255
0.576
0.528, 0.622
0.0017
134
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