Data from: Direct and indirect genetic and fine-scale location effects on breeding date in song sparrows

Quantifying direct and indirect genetic effects of interacting females and males on variation in jointly expressed life-history traits is central to predicting microevolutionary dynamics. However, accurately estimating sex-specific additive genetic variances in such traits remains difficult in wild populations, especially if related individuals inhabit similar fine-scale environments.
Breeding date is a key life-history trait that responds to environmental phenology and mediates individual and population responses to environmental change. However, no studies have estimated female (direct) and male (indirect) additive genetic and inbreeding effects on breeding date, and estimated the cross-sex genetic correlation, while simultaneously accounting for fine-scale environmental effects of breeding locations, impeding prediction of microevolutionary dynamics.
We fitted animal models to 38 years of song sparrow (Melospiza melodia) phenology and pedigree data to estimate sex-specific additive genetic variances in breeding date, and the cross-sex genetic correlation, thereby estimating the total additive genetic variance while simultaneously estimating sex-specific inbreeding depression. We further fitted three forms of spatial animal model to explicitly estimate variance in breeding date attributable to breeding location, overlap among breeding locations and spatial autocorrelation. We thereby quantified fine-scale location variances in breeding date and quantified the degree to which estimating such variances affected the estimated additive genetic variances.
The non-spatial animal model estimated nonzero female and male additive genetic variances in breeding date (sex-specific heritabilities: 0·07 and 0·02, respectively) and a strong, positive cross-sex genetic correlation (0·99), creating substantial total additive genetic variance (0·18). Breeding date varied with female, but not male inbreeding coefficient, revealing direct, but not indirect, inbreeding depression. All three spatial animal models estimated small location variance in breeding date, but because relatedness and breeding location were virtually uncorrelated, modelling location variance did not alter the estimated additive genetic variances.
Our results show that sex-specific additive genetic effects on breeding date can be strongly positively correlated, which would affect any predicted rates of microevolutionary change in response to sexually antagonistic or congruent selection. Further, we show that inbreeding effects on breeding date can also be sex specific and that genetic effects can exceed phenotypic variation stemming from fine-scale location-based variation within a wild population.

量化相互作用的雌雄个体对共同表达的生活史性状变异的直接与间接遗传效应，是预测微进化动力学（microevolutionary dynamics）的核心所在。然而，在野生种群中精准估算此类性状的性特异性加性遗传方差（additive genetic variance）仍颇具挑战，当亲缘个体栖息于相似的精细尺度环境中时，这一难度尤甚。
繁殖日期是响应环境物候、调控个体及种群对环境变化响应的关键生活史性状。然而，目前尚无研究在同时考量繁殖位点的精细尺度环境效应的前提下，估算繁殖日期的雌性（直接）与雄性（间接）加性遗传效应、近交效应，以及跨性遗传相关（cross-sex genetic correlation），这一现状阻碍了微进化动力学的预测。
我们将动物模型（animal model）应用于歌带鹀（Melospiza melodia）长达38年的物候与系谱数据（pedigree data），以估算繁殖日期的性特异性加性遗传方差与跨性遗传相关（cross-sex genetic correlation），进而在估算性特异性近交衰退（inbreeding depression）的同时，得到总加性遗传方差。我们进一步构建了三种形式的空间动物模型（spatial animal model），以明确估算由繁殖位点、繁殖位点重叠及空间自相关（spatial autocorrelation）所导致的繁殖日期方差。借此，我们量化了繁殖日期的精细尺度位点方差，并明确了估算此类方差对加性遗传方差估算结果的影响程度。
非空间动物模型（non-spatial animal model）估算得到繁殖日期存在显著的雌性与雄性加性遗传方差（性特异性遗传力（heritability）分别为0.07与0.02），且跨性遗传相关呈强正相关（0.99），由此产生了可观的总加性遗传方差（0.18）。繁殖日期随雌性近交系数（inbreeding coefficient）变化而显著波动，但与雄性近交系数无关，这表明存在直接而非间接的近交衰退。三种空间动物模型均估算得到繁殖日期的位点方差较小，但由于亲缘关系与繁殖位点几乎无相关性，对位点方差的建模并未改变加性遗传方差的估算结果。
本研究结果表明，繁殖日期的性特异性加性遗传效应可呈强正相关，这将影响针对性拮抗选择或协同选择的微进化变化预测速率。此外，我们证实繁殖日期的近交效应同样具有性特异性，且在野生种群中，遗传效应可超过由精细尺度位点变异所产生的表型变异。