Risky genetic rescue of the Helmeted Honeyeater

This is data for the manuscript published in <em>Biological Conservation </em>(2023): <strong>Benefits of genetic rescue of a critically endangered subspecies from another subspecies outweigh risks: results of captive breeding trials</strong> by Alexandra Pavlova, Sara Petrovic, Katherine A. Harrisson, Karina Cartwright, Elizabeth Dobson, Laura L. Hurley, Meagan Lane, Michael JL Magrath, Kimberly Miller, Bruce Quin, Monique Winterhoff, Jian D. L. Yen, and Paul Sunnucks <br> <br> The content of the files is as follows: <strong>risky_genetic_rescue_140223.R</strong> -- R script for running fitness models and plotting the results. All code is also available at https://doi.org/10.5281/zenodo.7735233 <br> <strong>TableS1_parents.xlsx</strong> -- Unique birds used in the breeding program (N=74), their sex, taxon, captive or wild origin, date of birth, and types of breeding pairs: unique pairs include each unique pair the bird was involved in once, non-unique pairs include multiple counts for pairs with the same partner in multiple breeding seasons. <br> <strong>TableS2_pairs_seasons_aviaries.xlsx</strong> -- Unique pairs (N=176), their pair type, sex-specific pair type and aviary size (L-large, M- medium) for each breeding season. <br> <strong>TableS3_first_time_pairs.csv</strong> -- First-time-pairs dataset: nest building outcomes for first time pairs. <br> <strong>TableS4_nests.csv</strong> -- Nest dataset: reproductive outcomes per nest. <br> Tables S5-S7 are values plotted on Fig1, Fig2, Appendix 4 and Appendix 5. Column "name" indicates which models the estimate is for: nestbuilt- M1, clutchsize-M2a, eggsfertile- M2b, hatchedeggs- M2c, chicksfledged- M2d, independentchicks- M2e, expected_independent_chicks_reduced_stages- cumulative probabilities. <br> <strong>TableS5_Fig1_Fig2_raw_values.csv </strong> -- Summary of Bayesian posterior probability values for all Bayesial models and cumulative probabilities used to build Fig.1 and Fig.2 of the main manuscript. <br> <strong>TableS6_Appdx4_raw_values_link_scale.csv</strong> -- Summary of Bayesian posterior probability values for all Bayesial models used to build plots in Appendix 4. All values are presented relative to CC, for which the value is zero. <br> <strong>TableS7_Appdx5_random_effect_raw_values.csv</strong> -- Deviations of an individual or group from the fitted value based on all other terms in the model, plotted in Appendix 5. These values should not be interpreted directly, as the modeled value reflects only realized outcomes (for example, the value for a specific DAM_ID shows how this individual's outcome deviates from the expected outcome given its cross type, breeding season, Sire_ID etc). <br> <strong>Supplementary_Data1_PairSummary.xlsx</strong> -- Pair-per-season dataset: summary of reproductive output for each pair, per breeding season (pairs bred in multiple seasons are listed multiple times). <br> We acknowledge Wurundjeri Woi Wurrung and Gunaikurnai People as Traditional Owners of the lands on which helmeted honeyeaters and Gippsland yellow-tufted honeyeaters occur.

本数据集对应2023年发表于《Biological Conservation》（《生物保护》）的学术论文：**《亚种间基因拯救极危亚种的收益大于风险：圈养繁殖试验结果》**，作者为Alexandra Pavlova、Sara Petrovic、Katherine A. Harrisson、Karina Cartwright、Elizabeth Dobson、Laura L. Hurley、Meagan Lane、Michael JL Magrath、Kimberly Miller、Bruce Quin、Monique Winterhoff、Jian D. L. Yen及Paul Sunnucks。

本次共享的数据集文件内容如下：
1. **risky_genetic_rescue_140223.R**：用于运行适合度模型（fitness models）并绘制结果的R脚本。所有代码亦可通过https://doi.org/10.5281/zenodo.7735233获取。
2. **TableS1_parents.xlsx**：记录了本繁殖项目中使用的74只独特个体鸟类的相关信息，包括性别、类群、圈养/野生来源、出生日期，以及繁殖配对类型：非重复配对指该鸟类仅与某一伴侣配对一次的情况，重复配对则指该鸟类在多个繁殖季与同一伴侣多次配对的情况。
3. **TableS2_pairs_seasons_aviaries.xlsx**：包含176组独特繁殖配对的信息，涵盖每个繁殖季的配对类型、性别特异性配对类型及笼舍规模（L代表大型，M代表中型）。
4. **TableS3_first_time_pairs.csv**：首次配对数据集：记录首次配对个体的筑巢结果。
5. **TableS4_nests.csv**：鸟巢数据集：记录每巢的繁殖结果。
6. 表S5至S7为主论文图1、图2、附录4及附录5的绘图原始数值。其中"name"列指示估计值对应的模型：筑巢（nestbuilt）对应M1模型，窝卵数（clutchsize）对应M2a模型，可育卵数（eggsfertile）对应M2b模型，出壳卵数（hatchedeggs）对应M2c模型，离巢雏鸟数（chicksfledged）对应M2d模型，独立雏鸟数（independentchicks）对应M2e模型，简化阶段下的预期独立雏鸟数（expected_independent_chicks_reduced_stages）对应累积概率。
7. **TableS5_Fig1_Fig2_raw_values.csv**：用于构建主论文图1与图2的所有贝叶斯模型（Bayesian models）后验概率（posterior probability）及累积概率汇总。
8. **TableS6_Appdx4_raw_values_link_scale.csv**：用于构建附录4绘图的所有贝叶斯模型后验概率值汇总。所有数值均以CC组为参照，其值设为0。
9. **TableS7_Appdx5_random_effect_raw_values.csv**：附录5绘图所用的基于模型中所有其他项计算得到的个体/组相对于拟合值的偏差值。此类数值不可直接解读：模型拟合值仅反映实际观测结果（例如，某DAM_ID对应的数值代表该个体的繁殖结果相较于其杂交类型、繁殖季、父本ID等条件下的预期结果的偏差）。
10. **Supplementary_Data1_PairSummary.xlsx**：逐季配对数据集：汇总每对繁殖个体在每个繁殖季的繁殖产出（在多个繁殖季参与繁殖的配对会被多次列出）。

本研究鸣谢Wurundjeri Woi Wurrung与Gunaikurnai族群，其为盔吸蜜鸟（helmeted honeyeaters）及吉普斯兰黄吸蜜鸟（Gippsland yellow-tufted honeyeaters）栖息土地的传统所有者。