Risky genetic rescue of the Helmeted Honeyeater

This is data for the manuscript published in Biological Conservation (2023): Benefits of genetic rescue of a critically endangered subspecies from another subspecies outweigh risks: results of captive breeding trials 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 The content of the files is as follows: risky_genetic_rescue_140223.R -- R script for running fitness models and plotting the results. All code is also available at https://doi.org/10.5281/zenodo.7735233 TableS1_parents.xlsx -- 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. TableS2_pairs_seasons_aviaries.xlsx -- Unique pairs (N=176), their pair type, sex-specific pair type and aviary size (L-large, M- medium) for each breeding season. TableS3_first_time_pairs.csv -- First-time-pairs dataset: nest building outcomes for first time pairs. TableS4_nests.csv -- Nest dataset: reproductive outcomes per nest. 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. TableS5_Fig1_Fig2_raw_values.csv -- 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. TableS6_Appdx4_raw_values_link_scale.csv -- 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. TableS7_Appdx5_random_effect_raw_values.csv -- 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). Supplementary_Data1_PairSummary.xlsx -- Pair-per-season dataset: summary of reproductive output for each pair, per breeding season (pairs bred in multiple seasons are listed multiple times). We acknowledge Wurundjeri Woi Wurrung and Gunaikurnai People as Traditional Owners of the lands on which helmeted honeyeaters and Gippsland yellow-tufted honeyeaters occur.

本数据集对应发表于《生物保护（Biological Conservation）》2023年的研究论文：异种间遗传拯救（genetic rescue）濒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以及Paul Sunnucks。

本数据集包含的文件内容如下：
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：收录本繁殖计划中使用的74只独特个体鸟类的相关信息，包括其性别、类群、圈养/野生来源、出生日期，以及繁殖配对类型：唯一配对指该个体参与过的每一组独特配对，非唯一配对指在多个繁殖季与同一伴侣配对的重复计数。
3. TableS2_pairs_seasons_aviaries.xlsx：收录176组独特繁殖配对的相关信息，包括每组配对的类型、按性别划分的配对类型，以及每个繁殖季对应的笼舍规模（L代表大、M代表中）。
4. TableS3_first_time_pairs.csv：首次配对数据集，包含首次配对个体的筑巢结果。
5. TableS4_nests.csv：鸟巢数据集，包含每个鸟巢的繁殖结果。
6. 表S5至S7为主论文图1、图2、附录4及附录5的绘图数据源。其中列"name"用于标识估计值对应的模型：nestbuilt（筑巢）对应M1，clutchsize（窝卵数）对应M2a，eggsfertile（受精卵数）对应M2b，hatchedeggs（孵出卵数）对应M2c，chicksfledged（出飞幼雏数）对应M2d，independentchicks（独立幼雏数）对应M2e，expected_independent_chicks_reduced_stages（简化阶段预期独立幼雏数，对应累积概率）。
7. TableS5_Fig1_Fig2_raw_values.csv：主论文图1和图2所用的所有贝叶斯后验概率（Bayesian posterior probability）值及累积概率汇总表。
8. TableS6_Appdx4_raw_values_link_scale.csv：附录4绘图所用的所有贝叶斯后验概率值汇总表。所有数值均以CC组为参照基准（CC组数值设为0）。
9. TableS7_Appdx5_random_effect_raw_values.csv：基于模型中所有其他项计算得到的个体或组与拟合值的偏差值，用于附录5绘图。此类数值不可直接解读，因模型值仅反映实际观测结果（例如，特定DAM_ID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等因素对应的预期结果的偏差）。
10. Supplementary_Data1_PairSummary.xlsx：逐季配对数据集，包含每个繁殖季中各组配对的繁殖产出汇总（多季繁殖的配对会被多次列出）。

本研究向Wurundjeri Woi Wurrung及Gunaikurnai原住民致敬，他们是盔吸蜜鸟（helmeted honeyeaters）与吉普斯兰黄吸蜜鸟（Gippsland yellow-tufted honeyeaters）栖息土地的传统所有者。