Data from: Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation

Numerous studies have reported associations between heterozygosity in microsatellite markers and fitness-related traits (heterozygosity-fitness correlations, HFCs). However, it has often been questioned whether HFCs reflect general inbreeding depression, because a small panel of microsatellite markers does not reflect very well an individual’s inbreeding coefficient (F) as calculated from a pedigree. Here we challenge this prevailing view. Due to chance events during Mendelian segregation, an individual’s realized proportion of the genome that is identical by descent (IBD) may substantially deviate from the pedigree-based expectation (i.e. F). This Mendelian noise may result in a weak correlation between F and multi-locus heterozygosity, but this does not imply that multi-locus heterozygosity is a bad estimator of realized IBD. We examined correlations between 11 fitness-related traits measured in up to 1,192 captive zebra finches and three measures of inbreeding: (1) heterozygosity across 11 microsatellite markers, (2) heterozygosity across 1,359 SNP markers, and (3) F, based on a 5-generation pedigree. All 11 phenotypic traits showed positive relationships with measures of heterozygosity, especially traits that are most closely related to fitness. Remarkably, the small panel of microsatellite markers produced equally strong HFCs as the large panel of SNP markers, and both marker-based approaches produced stronger correlations with phenotypes than the pedigree-based F. We argue that a small panel of microsatellites with high allelic richness may better reflect an individual’s realized IBD than previously appreciated, especially in species like the zebra finch, where much of the genome is inherited in large blocks that rarely experience cross-over during meiosis.

诸多研究均已报道微卫星标记（microsatellite markers）的杂合性与适合度相关性状之间存在关联，即杂合性-适合度相关性（heterozygosity-fitness correlations, HFCs）。然而，学界常对HFCs是否能反映普遍的近交衰退提出质疑，原因在于少量微卫星标记面板无法很好地反映通过系谱计算得到的个体近交系数（F）。在此我们对这一主流观点提出挑战。由于孟德尔分离（Mendelian segregation）过程中的随机事件，个体基因组中同祖同源（identical by descent, IBD）的实际比例可能与基于系谱的预期值（即F）存在显著偏差。这种孟德尔随机性噪声可能导致F与多位点杂合性之间仅存在微弱相关性，但这并不代表多位点杂合性并非实际IBD的优良估计量。本研究针对多达1192只圈养斑胸草雀测定的11项适合度相关性状，与3种近交衡量指标之间的相关性展开分析：（1）11个微卫星标记的杂合性；（2）1359个单核苷酸多态性（single nucleotide polymorphism, SNP）标记的杂合性；（3）基于5代系谱计算得到的F值。所有11项表型性状均与杂合性衡量指标呈现正相关关系，其中与适合度关联最为紧密的性状尤为显著。值得注意的是，少量微卫星标记面板所得到的HFCs强度与大规模SNP标记面板相当，且两种基于标记的分析方法所得出的表型相关性均强于基于系谱的F值。我们认为，相较于此前的认知，具备高等位基因丰富度（allelic richness）的少量微卫星标记面板或许能更准确地反映个体的实际IBD，尤其是在斑胸草雀这类物种中——其基因组大部分以大片段形式遗传，减数分裂过程中极少发生交叉互换（cross-over）。