Experimental demonstration of functional divergence in mitochondrial metabolism between two finch subspecies subjected to a thermal challenge
Data files
Jul 07, 2025 version files 6.28 GB
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masterdb5.csv
22.08 KB
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README.md
5.83 KB
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VCFs.zip
6.28 GB
Abstract
Different environments and climates can influence physiological variation and species’ geographic ranges. It has been suggested that mitochondria may play an essential role in this adaptation. We measured mitochondrial metabolism in two geographically separate subspecies of a songbird – the Long-tailed Finch, Poephila acuticauda - before and after ten days of heat exposure at 40°C. There were significant differences between subspecies, with the Red-billed P. a. hecki having lower proton leak and energy production efficiency than the Yellow-billed P. a. acuticauda, independent of treatment. Mitochondrial metabolism increased significantly after the heat treatment in five out of six variables in both subspecies, with P. a. hecki showing steeper reaction norms in metabolic acclimation to 40°C for the electron transport system. The heat treatment did not significantly increase circulating corticosterone, and at an individual level corticosterone and mitochondrial metabolism were unrelated. Eight out of nine climatic variables differed between subspecies’ geographical ranges, but whether these or other ecological variables explain the pre- and post-heat divergent mitochondrial performance requires further research. The reduced ETS metabolic flexibility of P. a. acuticauda after heat exposure suggests that future increases in the frequency and intensity of heat waves may impose asymmetric physiological costs on the two subspecies.
Dataset DOI: 10.5061/dryad.0zpc86757
Description of the data and file structure
The data attached was collected for the manuscript titled "Experimental demonstration of functional divergence in mitochondrial metabolism between two finch subspecies subjected to a thermal challenge", and includes real-time respirometry measurements collected before and after a heat challenge, corticosterone levels measurements, genetic divergence estimation and climatological data of the area where these two finch subspecies (i.e., Poephila acuticauda acuticauda and P. a. hecki) spread in the wild.
Files and variables
File: masterdb5.csv
Description: This dataset contains 150 observations for the two subspecies of finches (i.e. the Yellow-billed Poephila acuticauda acuticauda and the Red-billed P. a. hecki). More precisely, there are 87 observations for the red beaks, corresponding to 46 unique birds, and 63 observations for the yellow beaks, corresponding to 34 unique birds. For each colour, the birds have been assigned to two groups, control (identified as 25C) and treated (identified as 40C). For the reds, we have 15 birds assigned to the control group and 31 assigned to the treated group (of which 26 have observations after the treatment). For the yellows, we have 11 birds assigned to the control group and 23 assigned to the treated group (of which 18 have observations after the treatment).
Variables
- DATE: date indicating the date of the experiment (dd/mm/yy)
- SAMPLE_ID: numeric value indicating the unique ID for each sample
- BAND: factor indicating the unique bird ID (80 levels)
- TREAT: factor indicating control group (25°C) and treatment group (40°C)
- TREAT_TH: factor indicating whether the measurement has been taken before or after the treatment. In the case of the control group, the temperature is kept fixed at 25°C for both measurements. In the case of the treated group, the temperature is 25°C for the first measurement (Before), and 40°C for the second measurement (After).
- Bm: numeric value indicating the body mass (g) of the bird
- AGE: approximate bird age (days from hatching date)
- AGE_IN_YEARS: bird age (days rounded to years)
- AGE_GROUPED: birds age by hatching date (Y=young; M=medium; O=old)
- COLOUR: birds' beak colour (Y=yellow; R=red)
- CORT: numeric value indicating the corticosterone level (ng/ml)
- BASAL_CORT: factor indicating whether the measurement has been taken before three minutes (Y=under 3 minutes; N=over 3 minutes)
- CORT_PLATE: factor indicating the plate on which the corticosterone level has been measured (8 levels)
- BASELINE: numeric value indicating the basal mitochondrial oxygen consumption (pmol O2s-1 mL-1)
- P: numeric value indicating the basal mitochondrial oxygen consumption after a pyruvate injection (pmol O2s-1 mL-1)
- OMY: numeric value indicating the mitochondrial oxygen consumption related to proton leak (pmol O2s-1 mL-1)
- U: numeric value indicating the oxygen consumption during the electron transport system (pmol O2s-1 mL-1)
- PROT: numeric value indicating the sample protein content.
- OXPHOS_2: numeric value indicating the oxidative phosphorylation (pmol O2s-1 mL-1).
- OxCE: numeric value indicating the OxPhos coupling efficiency.
- FCR: numeric value indicating the mitochondrial reserve capacity.
- BLEEDING_TIME_SEC: numeric value indicating the bleeding time in seconds.
File: VCFs.zip
Description: To compare patterns of genetic divergence between the mitochondrial and nuclear genomes, we used the PopGenome package in R (Pfeifer et al., 2014). For the mitochondrial genome, we used a set of biallelic SNPs called from allopatric individuals of wild-caught Poephila acuticauda acuticauda (n = 14) and P. a. hecki (n = 11) (Methods described in McDiarmid et al., 2024). For the nuclear genome, we used a set of biallelic SNPs called from whole-genome re-sequencing of allopatric individuals of wild-caught acuticauda (n = 15) and hecki (n = 16) (Methods described in Hooper et al., 2024). We imported Variant Call Format (VCF) data for each of the 28 chromosomes greater than 5 Mb in length into PopGenome and calculated 𝜋 – i.e., the average pairwise nucleotide diversity within a population – for acuticauda and hecki separately using the diversity.stats function and calculated Dxy – i.e., the average pairwise nucleotide diversity between populations – using the diversity.stats.between function. We then obtained diversity estimates per-site by dividing PopGenome results by the total number of non-repeat masked sites on each chromosome. We obtained our autosomal estimate of 𝜋 and Dxy by summing pairwise differences and accessible sites across each of the 27 autosomal chromosomes analysed. Finally, we calculated the absolute genetic divergence (da) for the autosomes, Z chromosome, and the mitochondrial genome as da = 𝑑𝑥𝑦 ― (𝜋𝑥 + 𝜋𝑦)/2. This measure gives an estimate of absolute genetic divergence, taking into account genetic variation both within and between subspecies.
Code/software
Mitochondrial respiration data were obtained using the O2k real-time respirometer graphical user interface, DataLab 7.4 (Oroboros Instruments). Data analysis was performed in R, using the following packages: tidyverse, lmerTest, patchwork, effects, stargazer, xtable, latex2exp, ICC, lme4, dplyr, ggplot2, PopGenome.
The scripts used for mitochondrial data analysis are in the manuscript's Supplementary Materials, and the scripts for the genetic divergence estimation are in the VCFs.zip file attached to this repository.
The mitochondrial dataset was obtained using an O2k real-time respirometer (Oroboros Instruments). For details, see Materials and Methods.