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.

已有充分证据显示，近交衰退（inbreeding depression）会导致研究对象个体的适合度或与适合度相关的性状出现降低。在众多生物类群中，个体的适合度不仅受自身携带的基因影响，还会受亲本携带基因的调控——例如当个体接受亲本抚育时便会出现这类情况。尽管已有诸多研究在多个研究系统中报道了母体效应（maternal effects），但目前极少有研究同时考察近交衰退是直接通过研究对象个体，还是间接通过其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，因为其幼崽会接受长时间的母体抚育。本研究针对3个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）以及3个适合度组分（雄性当年存活率、成体年存活率与年度繁殖成功率），分别采用基于系谱推导的近交系数，以及基于约37000个单核苷酸多态性（Single Nucleotide Polymorphism，SNP）标记计算得到的基因组近交估算值，来检验母体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、雄性当年存活率，以及成体的年存活率与年度繁殖成功率均存在近交衰退现象。此外还发现母体近交可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，利用基因组估算值我们检测到了更多存在显著近交衰退的案例，这在一定程度上可归因于基因组分析可获得更大的有效样本量。综上，本研究结果表明，在存在亲本抚育的物种中，跨代近交效应值得进一步深入探究；同时也证实，在自然种群研究中，现代基因组学工具可成功替代系谱分析，或与系谱分析结合使用。