Data from: Genomic analysis reveals depression due to both individual and maternal inbreeding in a free-living mammal population

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.

已有充分证据表明，近交衰退（inbreeding depression）会表现为研究目标个体的适合度或与适合度相关性状的降低。在众多生物类群中，个体的适合度不仅受自身携带的基因调控，同时还受其亲本携带的基因影响，例如当存在亲本抚育行为时。尽管已有诸多研究系统报道了母性效应（maternal effects），但同时探究近交是直接通过目标个体，还是间接通过其亲本的近交系数（inbreeding coefficients）影响适合度的相关研究却极为匮乏。
索伊羊（Soay sheep）的野外研究种群是同时检验这两类效应的理想实验系统，因其幼崽会接受持久的母性抚育。本研究针对三项与适合度相关的性状（出生体重、4月龄体重及4月龄后肢长度）与三项适合度组分（出生后第一年存活率、成年个体年存活率及年度繁殖成功率），分别采用系谱推导的近交系数与基于约37000个单核苷酸多态性（SNP）标记计算的基因组近交估计值，检验了母性近交衰退与个体近交衰退效应。
研究结果显示，4月龄个体的后肢长度与体重、雄性个体的出生后第一年存活率，以及成年个体的年存活率与繁殖成功率均存在显著的近交衰退现象。母性近交则会显著降低幼崽的出生体重与4月龄体重。相较于系谱分析方法，我们通过基因组近交估计值检测到了更多存在显著近交衰退的案例，这一差异部分可归因于基因组方法可获得更大的样本量。
综上，本研究结果表明，跨代近交效应值得在存在亲本抚育的物种中开展进一步探究，且在自然种群研究中，现代基因组工具可成功替代系谱方法，或与其结合使用。