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

AbstractQuantifying 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., Usage notesMain_DatasetThis file contains the phenotypic data for the joint univariate animal model analysis of breeding date.Numeric_PedigreeThis file contains the numeric pedigree used to construct the inverted A (relationship) matrix for the joint univariate animal model analysis of breeding date.Unique_ID_All_Cell_SizesThis file contains the identity of each grid cell a given nest was located in for each version of the 'Grid' joint univariate animal model analysis of breeding date presented in the above paper.Overlap_Buff_50m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 50m^2) used to construct the S matrix for the '50 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_100m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 100m^2) used to construct the S matrix for the '100 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_150m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 150m^2) used to construct the S matrix for the '150 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_200m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 200m^2) used to construct the S matrix for the '200 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_250m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 250m^2) used to construct the S matrix for the '250 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_300m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 300m^2) used to construct the S matrix for the '300 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_400m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 400m^2) used to construct the S matrix for the '400 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_500m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 500m^2) used to construct the S matrix for the '500 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_600m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 600m^2) used to construct the S matrix for the '600 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_700m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 700m^2) used to construct the S matrix for the '700 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_800m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 800m^2) used to construct the S matrix for the '800 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_900m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 900m^2) used to construct the S matrix for the '900 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_1000m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 1000m^2) used to construct the S matrix for the '1000 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_1500m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 1500m^2) used to construct the S matrix for the '1500 m overlap' animal model presented in the supporting information of the above paperOverlap_Buff_2000m_All_NestsThis file contains a list of all overlapping nest buffers (buffer area = 2000m^2) used to construct the S matrix for the '2000 m overlap' animal model presented in the supporting information of the above paper

摘要：量化交互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，是预测微观进化动力学的核心任务。然而，在野生种群中准确估算此类性状的性别特异性加性遗传方差仍颇具挑战，尤其是当亲缘个体栖息于相似的精细尺度环境中时。繁殖日期是关键的生活史性状，其响应环境物候变化，并介导个体与种群对环境变化的响应。但目前尚无研究在同时考量繁殖地点的精细尺度环境效应的前提下，估算雌性（直接）与雄性（间接）对繁殖日期的加性遗传效应与近交效应，以及跨性别遗传相关性，这阻碍了微观进化动力学的预测。我们针对歌带鹀（Melospiza melodia）38年的物候与谱系数据拟合动物模型（animal model），以估算繁殖日期的性别特异性加性遗传方差与跨性别遗传相关性，进而估算总加性遗传方差，同时估算性别特异性近交衰退。我们进一步拟合三种空间动物模型，以明确估算由繁殖地点、繁殖地点间重叠度与空间自相关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地点方差，并评估了估算此类方差对加性遗传方差估计结果的影响程度。非空间动物模型估算得到繁殖日期存在显著的雌性与雄性加性遗传方差（性别特异性遗传率分别为0.07与0.02），以及较强的正向跨性别遗传相关性（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变化而变化，但与雄性近交系数无关，这揭示了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地点方差较小，但由于亲缘关系与繁殖地点几乎无相关性，建模地点方差并未改变加性遗传方差的估计结果。我们的研究结果表明，繁殖日期的性别特异性加性遗传效应可呈现强正向相关性，这将影响针对性拮抗或性一致选择所预测的微观进化变化速率。此外，我们证明了繁殖日期的近交效应同样具有性别特异性，且在野生种群中，遗传效应可超过由精细尺度地点差异所产生的表型变异。

使用说明
Main_Dataset：本文件包含用于繁殖日期联合单变量动物模型分析的表型数据。
Numeric_Pedigree：本文件包含用于构建繁殖日期联合单变量动物模型分析的逆A（亲缘关系）矩阵的数值谱系数据。
Unique_ID_All_Cell_Sizes：本文件包含上述论文中提出的各版本「Grid」繁殖日期联合单变量动物模型分析中，每个鸟巢所在的网格单元编号。
Overlap_Buff_50m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=50平方米）的列表，用于构建上述论文补充材料中「50 m重叠」动物模型的S矩阵。
Overlap_Buff_100m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=100平方米）的列表，用于构建上述论文补充材料中「100 m重叠」动物模型的S矩阵。
Overlap_Buff_150m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=150平方米）的列表，用于构建上述论文补充材料中「150 m重叠」动物模型的S矩阵。
Overlap_Buff_200m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=200平方米）的列表，用于构建上述论文补充材料中「200 m重叠」动物模型的S矩阵。
Overlap_Buff_250m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=250平方米）的列表，用于构建上述论文补充材料中「250 m重叠」动物模型的S矩阵。
Overlap_Buff_300m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=300平方米）的列表，用于构建上述论文补充材料中「300 m重叠」动物模型的S矩阵。
Overlap_Buff_400m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=400平方米）的列表，用于构建上述论文补充材料中「400 m重叠」动物模型的S矩阵。
Overlap_Buff_500m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=500平方米）的列表，用于构建上述论文补充材料中「500 m重叠」动物模型的S矩阵。
Overlap_Buff_600m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=600平方米）的列表，用于构建上述论文补充材料中「600 m重叠」动物模型的S矩阵。
Overlap_Buff_700m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=700平方米）的列表，用于构建上述论文补充材料中「700 m重叠」动物模型的S矩阵。
Overlap_Buff_800m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=800平方米）的列表，用于构建上述论文补充材料中「800 m重叠」动物模型的S矩阵。
Overlap_Buff_900m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=900平方米）的列表，用于构建上述论文补充材料中「900 m重叠」动物模型的S矩阵。
Overlap_Buff_1000m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=1000平方米）的列表，用于构建上述论文补充材料中「1000 m重叠」动物模型的S矩阵。
Overlap_Buff_1500m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=1500平方米）的列表，用于构建上述论文补充材料中「1500 m重叠」动物模型的S矩阵。
Overlap_Buff_2000m_All_Nests：本文件包含所有重叠鸟巢缓冲区（缓冲区面积=2000平方米）的列表，用于构建上述论文补充材料中「2000 m重叠」动物模型的S矩阵。