Data from: Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages

# Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages [https://doi.org/10.5061/dryad.m37pvmd9v](https://doi.org/10.5061/dryad.m37pvmd9v) We have submitted our raw aerobic metabolism data (**aerobic_metabolism_data.csv**), embryonic heart rate data (**heart_rate.csv**), mitochondrial copy number data (**mitochondrial_copy_number.csv**), oxidative damage data (**oxidative_damage.csv**), and an R script for analyzing the datasets used in this study (**aerobic_metabolism_analyses_annotated_.R**). ## Descriptions ### aerobic\_metabolism\_data * *Egg*: Individual embryo ID number * *Dup*: An embryo that was measured multiple times as a technical replicate is marked 'DUP' * *Sex*: Sex of embryo * male * female * *OXPI*: Oxidative phosphorylation when only complex I (CxI) is receiving electrons (coupled respiration measurement) * *OXPI_II*: Coupled respiration capacity through both complex I (CxI) and complex II (CxII) (coupled respiration measurement) * *LEAK_II*: Oxygen consumption associated with proton leak when electrons are being received by both complex I (CxI) and complex II (CxII) (proton leak measurement) * *ETSI_II*: Maximum capacity of electron transport system (uncoupled respiration measurement) * *ETSII*: Capacity of electron transport system when only receiving electrons from complex II (CxII) * *CXIV*: Respiration capacity of complex IV (CxIV) (maximum respiration measurement) * *OXPI_tlength*: Measurement time for *OXPI* (seconds) * *OXPI_II_tlength*: Measurement time for *OXPI_II* (seconds) * *LEAKI_II_tlength*: Measurement time for *LEAK_II* (seconds) * *ETSI_II_tlength* : Measurement time for *ETSI_II* (seconds) * *ETSII_tlength*: Measurement time for *ETSII* (seconds) * *AsTM_tlength*: Measurment time for *AsTM* (seconds) * *EmbryoMass*: Mass of embryo (grams) * *PairID*: Breeding pair ID number combining maternal and paternal ID numbers * *FemID*: Maternal ID number * *PairType*: Experimental cross type * 01_acuM_acuN: Offspring of *acuticauda* parents (**mitoconcordant** parental) * 02_hecM_hecN: Offspring of *hecki* parents (**mitoconcordant** parental) * 03_acuM_acuN: Offspring of *acuticauda* mtDNA carrying F1 female and an *acuticauda* male (**mitoconcordant** backcross *acuticauda*) * 04_hecM_hecN: Offspring of *hecki* mtDNA carrying F1 female and a *hecki* male (**mitoconcordant** backcross *hecki*) * 05_acuM_hecN: Offspring of *acuticauda* mtDNA carrying F1 female and a *hecki* male (**mitodiscordant** backcross *acuticauda*) * 06_hecM_acuN: Offspring of *hecki* mtDNA carrying F1 female and an *acuticauda* male (**mitodiscordant** backcross *hecki*) * *ProtCont*: Protein quantity ### heart\_rate * *Egg*: Individual embryo ID number * *Sex*: Sex of embryo * male * female * *PairID*: Breeding pair ID number combining maternal and paternal ID numbers * *PairType*: Experimental cross type * 01_acuM_acuN: Offspring of *acuticauda* parents (**mitoconcordant** parental) * 02_hecM_hecN: Offspring of *hecki* parents (**mitoconcordant** parental) * 03_acuM_acuN: Offspring of *acuticauda* mtDNA carrying F1 female and an *acuticauda* male (**mitoconcordant** backcross *acuticauda*) * 04_hecM_hecN: Offspring of *hecki* mtDNA carrying F1 female and a *hecki* male (**mitoconcordant** backcross *hecki*) * 05_acuM_hecN: Offspring of *acuticauda* mtDNA carrying F1 female and a *hecki* male (**mitodiscordant** backcross *acuticauda*) * 06_hecM_acuN: Offspring of *hecki* mtDNA carrying F1 female and an *acuticauda* male (**mitodiscordant** backcross *hecki*) * *N_measures*: Number of heart rate measurements taken and averaged * *Int*: Time spent outside of incubator (seconds) * *y_at_60*: Predicted heart rate after 60 seconds of cooling (beats per minute) ### mitochondrial\_copy\_number * *Egg*: Individual embryo ID number * *Sex*: Sex of embryo * male * female * *PairID*: Breeding pair ID number combining maternal and paternal ID numbers * *PairType*: Experimental cross type * 01_acuM_acuN: Offspring of *acuticauda* parents (**mitoconcordant** parental) * 02_hecM_hecN: Offspring of *hecki* parents (**mitoconcordant** parental) * 03_acuM_acuN: Offspring of *acuticauda* mtDNA carrying F1 female and an *acuticauda* male (**mitoconcordant** backcross *acuticauda*) * 04_hecM_hecN: Offspring of *hecki* mtDNA carrying F1 female and a *hecki* male (**mitoconcordant** backcross *hecki*) * 05_acuM_hecN: Offspring of *acuticauda* mtDNA carrying F1 female and a *hecki* male (**mitodiscordant** backcross *acuticauda*) * 06_hecM_acuN: Offspring of *hecki* mtDNA carrying F1 female and an *acuticauda* male (**mitodiscordant** backcross *hecki*) * *Plate*: Plate ID * *mtCN*: Estimated mitochondrial copy number ### oxidative\_damage * *Egg*: Individual embryo ID number * *Sex*: Sex of embryo * male * female * *PairID*: Breeding pair ID number combining maternal and paternal ID numbers * *PairType*: Experimental cross type * 01_acuM_acuN: Offspring of *acuticauda* parents (**mitoconcordant** parental) * 02_hecM_hecN: Offspring of *hecki* parents (**mitoconcordant** parental) * 03_acuM_acuN: Offspring of *acuticauda* mtDNA carrying F1 female and an *acuticauda* male (**mitoconcordant** backcross *acuticauda*) * 04_hecM_hecN: Offspring of *hecki* mtDNA carrying F1 female and a *hecki* male (**mitoconcordant** backcross *hecki*) * 05_acuM_hecN: Offspring of *acuticauda* mtDNA carrying F1 female and a *hecki* male (**mitodiscordant** backcross *acuticauda*) * 06_hecM_acuN: Offspring of *hecki* mtDNA carrying F1 female and an *acuticauda* male (**mitodiscordant** backcross *hecki*) * *ngDNA*: Quantity of DNA (nanograms) * *ODav*: Primary measurement of 8-OHdG (8-hydroxy-2’-deoxyguanosine) * *Run*: Run ID * *OSperc*: Secondary measurement of 8-OHdG (8-hydroxy-2’-deoxyguanosine) ## Supplemental Tables Supplemental tables S1-S4 are available through an open access agreement with Molecular Ecology. ## Sequence Data * The WGS data used to assemble mitochondrial genomes is available via SRA under the BioProject accession PRJNA1101033. * The mitochondrial genome assemblies used in this project are available via GenBenk under the accessions PP372643-PP372678. ## Code/Software R is required to run *aerobic_metabolism_analyses_annotated_.R*. The script was created using R version 4.1.2 and was used to create plots in Figure 5 and supplemental Figures 2 and 3.

# 线粒体核互作（Mitonuclear interactions）影响杂交个体的有氧代谢，或可解释年轻自然杂交鸟类谱系中的核线粒体不协调现象 [https://doi.org/10.5061/dryad.m37pvmd9v]
本研究已上传原始有氧代谢数据（**aerobic_metabolism_data.csv**）、胚胎心率数据（**heart_rate.csv**）、线粒体拷贝数数据（**mitochondrial_copy_number.csv**）、氧化损伤数据（**oxidative_damage.csv**），以及本研究数据分析所用的R脚本（**aerobic_metabolism_analyses_annotated_.R**）。
## 数据说明
### 有氧代谢数据
* *Egg*：单个胚胎编号
* *Dup*：多次测量作为技术重复的胚胎标记为'DUP'
* *Sex*：胚胎性别，可选值为male（雄性）、female（雌性）
* *OXPI*：仅复合物I（CxI，Complex I）接收电子时的氧化磷酸化水平（偶联呼吸测量值）
* *OXPI_II*：复合物I（CxI）与复合物II（CxII）共同接收电子时的偶联呼吸能力（偶联呼吸测量值）
* *LEAK_II*：复合物I与II共同接收电子时，质子漏相关的耗氧量（质子漏测量值）
* *ETSI_II*：电子传递系统的最大容量（解偶联呼吸测量值）
* *ETSII*：仅由复合物II（CxII）提供电子时的电子传递系统容量
* *CXIV*：复合物IV（CxIV）的呼吸能力（最大呼吸测量值）
* *OXPI_tlength*：OXPI的测量时长（秒）
* *OXPI_II_tlength*：OXPI_II的测量时长（秒）
* *LEAKI_II_tlength*：LEAK_II的测量时长（秒）
* *ETSI_II_tlength*：ETSI_II的测量时长（秒）
* *ETSII_tlength*：ETSII的测量时长（秒）
* *AsTM_tlength*：AsTM的测量时长（秒）
* *EmbryoMass*：胚胎质量（克）
* *PairID*：结合父母本编号的繁育对编号
* *FemID*：母本编号
* *PairType*：实验杂交类型：
* 01_acuM_acuN：*acuticauda*亲本的后代（**核线粒体协调（mitoconcordant）**亲本型）
* 02_hecM_hecN：*hecki*亲本的后代（**核线粒体协调**亲本型）
* 03_acuM_acuN：携带*acuticauda*线粒体DNA的F1雌性与*acuticauda*雄性的后代（**核线粒体协调**回交*acuticauda*型）
* 04_hecM_hecN：携带*hecki*线粒体DNA的F1雌性与*hecki*雄性的后代（**核线粒体协调**回交*hecki*型）
* 05_acuM_hecN：携带*acuticauda*线粒体DNA的F1雌性与*hecki*雄性的后代（**核线粒体不协调（mitodiscordant）**回交*acuticauda*型）
* 06_hecM_acuN：携带*hecki*线粒体DNA的F1雌性与*acuticauda*雄性的后代（**核线粒体不协调**回交*hecki*型）
* *ProtCont*：蛋白含量
### 胚胎心率数据
* *Egg*：单个胚胎编号
* *Sex*：胚胎性别，可选值为male（雄性）、female（雌性）
* *PairID*：结合父母本编号的繁育对编号
* *PairType*：实验杂交类型（同有氧代谢数据中的定义）
* *N_measures*：用于取平均的心率测量次数
* *Int*：移出孵化器的时长（秒）
* *y_at_60*：冷却60秒后的预测心率（每分钟心跳数）
### 线粒体拷贝数数据
* *Egg*：单个胚胎编号
* *Sex*：胚胎性别，可选值为male（雄性）、female（雌性）
* *PairID*：结合父母本编号的繁育对编号
* *PairType*：实验杂交类型（同前）
* *Plate*：微孔板编号
* *mtCN*：估算的线粒体拷贝数
### 氧化损伤数据
* *Egg*：单个胚胎编号
* *Sex*：胚胎性别，可选值为male（雄性）、female（雌性）
* *PairID*：结合父母本编号的繁育对编号
* *PairType*：实验杂交类型（同前）
* *ngDNA*：DNA总量（纳克）
* *ODav*：8-羟基脱氧鸟苷（8-hydroxy-2’-deoxyguanosine，8-OHdG）的一级测量值
* *Run*：实验批次编号
* *OSperc*：8-羟基脱氧鸟苷的二级测量值
## 补充表格
补充表格S1-S4可通过与*Molecular Ecology*达成的开放获取协议获取。
## 序列数据
* 本研究用于组装线粒体基因组的全基因组测序（WGS，Whole Genome Sequencing）数据可通过SRA获取，BioProject收录号为PRJNA1101033。
* 本项目所用的线粒体基因组组装序列可通过GenBank获取，收录号为PP372643-PP372678。
## 代码与软件
* 运行**aerobic_metabolism_analyses_annotated_.R**需要R语言环境。本脚本基于R 4.1.2版本编写，用于生成图5以及补充图2、3。