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Supporting Information for:
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Female mating preferences and offspring survival: testing hypotheses on the genetic basis of mate
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choice in a wild lekking bird
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Rebecca J. Sardell, Bart Kempenaers, and Emily H. DuVal
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Section S1: Choice of heterozygosity measure
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Heterozygosity can be measured in numerous ways: multilocus heterozygosity (MLH), which is the
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number of heterozygous loci divided by the number of locus typed; standardised heterozygosity (SH),
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which divides the proportion of heterozygous loci by the mean heterozygosity of loci to account for the
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fact that not all loci were typed in all individuals (Coltman et al. 1999); internal relatedness (IR), which is
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a measure of genetic diversity within individuals that is weighted by the frequency of alleles in the
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population; (Amos et al. 2001); and homozygosity by loci (HL), which takes into account rare alleles and
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weighs measures based on the frequency of each locus rather than allele (Aparicio et al. 2006). Here we
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calculated IR, SH and HL using the R-package Rhh. Because all three measures were highly correlated
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with MLH (R=0.96-0.99), we used MLH to avoid pseudoreplication as recommended in (Chapman et al.
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2009).
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Correlation in H across loci
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To measure the correlation in heterozygosity over loci (known as identity disequilibrium, ID) and hence
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potential for our set of microsatellites to determine whether effects of heterozygosity occurred throughout
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the genome, rather than at a few highly influential loci, within-individual heterozygosity- heterozygosity
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correlations were simulated. For this purpose we used the R-package Rhh to repeatedly and randomly
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divide the set of loci into two 1000 times and calculate heterozygosity measures for each subset (Balloux
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et al. 2004; Alho et al. 2010). Correlation between subsets of loci indicated a weak, but significant
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positive association between loci.
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number=1000) across 1993 individuals genotyped at ≥10 loci, while HL gave a correlation of r=0.05
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(CI=0.02-0.09) and IR gave r= 0.05 (CI=0.02-0.08).
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heterozygosity, strong correlation between heterozygosity measures implies heterozygosity would give
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similar results. We also quantified g2, a more powerful measure of inbreeding as recommended in (Slate
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et al. 2004; Szulkin et al. 2010) using RMES available at http://www.cefe.cnrs.fr (David et al. 2007).
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This also showed a significant, but weak correlation in heterozygosity over loci (ID g2=0.002, SD=0.001,
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p=0.003, n=1993, based on 1000 iterations). These correlations suggest that any HFC is likely to reflect
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genome-wide heterozygosity effects rather than associative overdominance.
SH gave a correlation of r=0.04 (95% CI=0.00-0.07, iteration
Although this method was not available for
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References
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Alho JS, Välimäki K, Merilä J (2010) Rhh: an R extension for estimating multilocus heterozygosity and
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heterozygosity–heterozygosity correlation. Molecular Ecology Resources, 10, 720-722.
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Amos W, Wilmer JW, Fullard K, et al (2001) The influence of parental relatedness on reproductive
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success. Proceedings of the Royal Society of London.Series B: Biological Sciences, 268, 2021-2027.
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Aparicio J, Ortego J, Cordero P (2006) What should we weigh to estimate heterozygosity, alleles or loci?
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Molecular ecology, 15, 4659-4665.
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Balloux F, Amos W, Coulson T (2004) Does heterozygosity estimate inbreeding in real populations?
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Molecular ecology, 13, 3021-3031.
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Chapman J, Nakagawa S, Coltman D, Slate J, Sheldon B (2009) A quantitative review of heterozygosity–
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fitness correlations in animal populations. Molecular ecology, 18, 2746-2765.
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Coltman DW, Pilkington JG, Smith JA, Pemberton JM (1999) Parasite-mediated selection against inbred
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Soay sheep in a free-living, island population. Evolution, 53, 1259-1267.
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David P, Pujol BIT, Viard F, Castella V, Goudet J (2007) Reliable selfing rate estimates from imperfect
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population genetic data. Molecular ecology, 16, 2474-2487.
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Slate J, David P, Dodds K, et al (2004) Understanding the relationship between the inbreeding coefficient
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and multilocus heterozygosity: theoretical expectations and empirical data. Heredity, 93, 255-265.
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Szulkin M, Bierne N, David P (2010) Heterozygosity-fitness correlations: a time for reappraisal.
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Evolution, 64, 1202-1217.
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Table S1
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Some females mated with >1 male in each year, therefore we repeated randomization tests comparing the
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mean and variance of Robs with the mean and variance of a distribution of Rexp values described in the
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main document by using a) the least related mate, b) the most related mate and c) all mates per female to
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calculate mean Robs and hence determine whether conclusions were robust. Years where the significance
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level (p) changed from those presented in the main document are highlighted in bold.
year
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
All
a)
Robs
-0.08
-0.04
0.00
-0.02
0.00
-0.03
-0.04
-0.07
-0.04
-0.09
-0.05
-0.06
-0.08
p
0.06
0.63
0.87
0.63
0.61
0.59
0.26
0.05
0.26
0.02
0.02
0.04
0.00
b)
Robs
-0.08
-0.02
0.01
0.02
0.01
-0.01
-0.02
-0.04
-0.02
-0.06
-0.03
-0.04
0.03
p
0.06
0.82
0.63
0.45
0.47
0.77
0.85
0.49
0.83
0.43
0.12
0.14
0.00*
c)
Robs
-0.08
-0.03
0.00
0.00
-0.02
-0.03
-0.03
-0.05
-0.03
-0.07
-0.05
-0.05
-0.04
p
0.06
0.88
0.83
0.95
0.82
0.59
0.36
0.28
0.49
0.14
0.03
0.06
0.02
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*Note that in this case, Robs was significantly higher than Rexp (mates were more related than expected).
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Table S2 Results from GLMMs explaining variation in alpha male annual reproductive success (RS) with
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respect to heterozygosity when known predictors age, year of alpha tenure, beta status, and final year of
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life were included. Random effects of male ID and year were included in models 1 and 2. Estimates,
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standard errors, and p-values are based on likelihood ratio tests. Significance for main effects of terms
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included in interactions is not presented. Terms included in the final model are highlighted in bold.
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Model
1. Annual RS (# offspring)
2.
Annual RS (≥1 offspring)
Excluded terms
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Term
Intercept
Age
Age2
Year of tenure
Beta (Y)
Final year
Beta * final year
H
Intercept
Age
Age2
Year of tenure
Beta (Y)
Final year
H
Beta * final year
estimate
-5.32
0.79
-0.04
0.19
0.51
0.51
-1.63
2.68
-6.88
1.59
-0.08
0.58
0.67
-0.54
1.08
-1.37
SE
1.73
0.32
0.02
0.09
0.30
0.31
0.45
1.05
3.02
0.69
0.04
0.22
0.51
0.51
2.05
0.99
LRT
p-value
6.16
5.31
4.94
13.09
6.36
0.01
0.02
0.03
<0.01
0.01
5.18
4.07
8.43
1.72
1.12
0.27
1.80
0.02
0.04
0.01
0.19
0.29
0.60
0.18
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Figure S1 Male annual reproductive success (RS, a) and male lifetime RS (b) measured as number of
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chicks sired positively correlated with mating success (the number of females with which a male sired
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young) in a year rs=0.93, p<0.01 (a) and in a lifetime rs=0.95, p<0.01 (b).
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Figure S2 The predicted correlation between the probability of offspring survival to recruitment and
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father annual reproductive success (RS) is shown by the solid line. Dashed lines represent 95%
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confidence intervals based on fixed effects only. Points show the jittered raw data. The relationship
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between annual success and survival to recruitment missed conventional statistical significance at p =
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0.07.
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Figure S3 Pairwise relatedness (R) was negatively correlated with both male heterozygosity (a) and
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female heterozygosity (b) while offspring heterozygosity was positively correlated with both father
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heterozygosity (c), and mother heterozygosity (d). Point sizes represent sample size. The solid line
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represents predicted values and the dashed lines 95% confidence intervals based on fixed effects only.
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