Heterogeneity of genetic architecture of body size traits in a free‐living population

Bérénos, Camillo; Ellis, Philip A; Pilkington, Jill G.; Lee, Sang; Gratten, Jacob; Pemberton, Josephine M.

doi:10.1111/mec.13146

Cited by 76 publications

(128 citation statements)

References 60 publications

(146 reference statements)

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“…For models analysing fitness components, in addition to the individual and maternal inbreeding coefficient, fixed effects for the focal individuals were chosen based on Bérénos et al . () and Johnston et al . () and subsequent exploratory analyses (for a full list of fixed effects fitted, please see Table S3, Supporting information).…”

Section: Methodsmentioning

confidence: 86%

Genomic analysis reveals depression due to both individual and maternal inbreeding in a free‐living mammal population

Bérénos¹,

Ellis²,

Pilkington³

et al. 2016

Molecular Ecology

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105

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There is ample evidence for inbreeding depression manifested as a reduction in fitness or fitness‐related traits in the focal individual. In many organisms, fitness is not only affected by genes carried by the individual, but also by genes carried by their parents, for example if receiving parental care. While maternal effects have been described in many systems, the extent to which inbreeding affects fitness directly through the focal individual, or indirectly through the inbreeding coefficients of its parents, has rarely been examined jointly. The Soay sheep study population is an excellent system in which to test for both effects, as lambs receive extended maternal care. Here, we tested for both maternal and individual inbreeding depression in three fitness‐related traits (birthweight and weight and hindleg length at 4 months of age) and three fitness components (first‐year survival, adult annual survival and annual breeding success), using either pedigree‐derived inbreeding or genomic estimators calculated using ~37 000 SNP markers. We found evidence for inbreeding depression in 4‐month hindleg and weight, first‐year survival in males, and annual survival and breeding success in adults. Maternal inbreeding was found to depress both birthweight and 4‐month weight. We detected more instances of significant inbreeding depression using genomic estimators than the pedigree, which is partly explained through the increased sample sizes available. In conclusion, our results highlight that cross‐generational inbreeding effects warrant further exploration in species with parental care and that modern genomic tools can be used successfully instead of, or alongside, pedigrees in natural populations.

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Section: Methodsmentioning

confidence: 86%

Genomic analysis reveals depression due to both individual and maternal inbreeding in a free‐living mammal population

Bérénos¹,

Ellis²,

Pilkington³

et al. 2016

Molecular Ecology

Self Cite

105

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“…) and leg length traits in Soay sheep (Bérénos et al . ), although it should be noted that these loci explain a minor proportion of total heritability. Further, the use of genomic relatedness is likely to offer a promising approach for estimating heritabilities in wild populations when pedigrees may be incomplete or incorrect, and may also allow for more accurate estimation of maternal effects (Bérénos et al .…”

Section: Discussionmentioning

confidence: 99%

Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

et al. 2015

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Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations.

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“…For example, Bérénos and colleagues calculated selection coefficients based on selection for survival, reproductive success, and overall lifetime fitness (Bérénos et al . ). We included the measures of selection on survival and reproductive success, but did not include the lifetime fitness selection coefficients in our quantitative analysis.…”

Section: Methodsmentioning

confidence: 97%

The genetic consequences of selection in natural populations

Thurman

Barrett

2016

Molecular Ecology

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The selection coefficient, s, quantifies the strength of selection acting on a genetic variant. Despite this parameter's central importance to population genetic models, until recently we have known relatively little about the value of s in natural populations. With the development of molecular genetic techniques in the late 20th century and the sequencing technologies that followed, biologists are now able to identify genetic variants and directly relate them to organismal fitness. We reviewed the literature for published estimates of natural selection acting at the genetic level and found over 3000 estimates of selection coefficients from 79 studies. Selection coefficients were roughly exponentially distributed, suggesting that the impact of selection at the genetic level is generally weak but can occasionally be quite strong. We used both nonparametric statistics and formal random-effects meta-analysis to determine how selection varies across biological and methodological categories. Selection was stronger when measured over shorter timescales, with the mean magnitude of s greatest for studies that measured selection within a single generation. Our analyses found conflicting trends when considering how selection varies with the genetic scale (e.g., SNPs or haplotypes) at which it is measured, suggesting a need for further research. Besides these quantitative conclusions, we highlight key issues in the calculation, interpretation, and reporting of selection coefficients and provide recommendations for future research.

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Heterogeneity of genetic architecture of body size traits in a free‐living population

Cited by 76 publications

References 60 publications

Genomic analysis reveals depression due to both individual and maternal inbreeding in a free‐living mammal population

Genomic analysis reveals depression due to both individual and maternal inbreeding in a free‐living mammal population

Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

The genetic consequences of selection in natural populations

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