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）会使目标个体的适合度或适合度相关性状出现下降。在诸多生物类群中，个体适合度不仅受自身携带的基因调控，也会受到亲本携带基因的影响——例如当个体接受亲本抚育时，便会出现这类效应。尽管已有诸多研究系统报道了母体效应，但目前极少有研究同时探究：近交衰退是直接通过目标个体自身，还是间接通过亲本的近交系数来影响适合度的程度。索艾羊（Soay sheep）研究种群是同时检验这两类效应的理想模型，因其羔羊会接受长时间的母体抚育。本研究针对三项适合度相关性状（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（当年存活率、成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（single nucleotide polymorphism, SNP）标记计算的基因组近交估算值，检验了母体与个体层面的近交衰退效应。研究结果显示，4月龄后肢长度与体重、雄性当年存活率，以及成体年存活率与繁殖成功率均存在显著的近交衰退效应。同时发现母体近交同样会降低子代的出生体重与4月龄体重。相较于系谱数据，基于基因组估算值我们检测到了更多存在显著近交衰退的性状，这一差异可部分由更大的可用样本量得到解释。综上，本研究结果表明，在存在亲本抚育的物种中，跨代近交效应亟待进一步探究；同时也证实，在自然种群中可借助现代基因组学工具替代或补充系谱数据开展相关研究。