Data and code from: Mechanisms underlying tolerance of severe hypoxia in sulfide spring fish
Data files
Jun 25, 2026 version files 72.79 MB
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2023_H2S_H_exposuretranscriptomics_Williams.xlsx
22.57 KB
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2024CR_ExposureExperiment.xlsx
15 KB
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counts_matrix_cr.txt
33.38 MB
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counts_matrix_mx.txt
30.18 MB
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CR_Key.xlsx
11.15 KB
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field_RNA_all_genename_2.Rmd
79.41 KB
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go_hypoxia_genes.xlsx
39.83 KB
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Hematocrit_Data_Field_2015.xlsx
12.95 KB
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hematocrit.Rmd
3.09 KB
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hypcounts.csv
5.78 MB
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hypdata.csv
9.54 KB
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Hypoxia_envdata.xlsx
13.45 KB
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Hypoxia_LOE_pilot_datasheets.xlsx
13.77 KB
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mexico_2024_LOE.xlsx
24.10 KB
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README.md
8.45 KB
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SampleKey_Hypoxia.xlsx
15.36 KB
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survivalanalysismex.Rmd
13.31 KB
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Table_S2-Poecilia_mexicana_Annotations_1.csv
3.09 MB
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WGCNA_2.Rmd
77.30 KB
Abstract
Isolating the causative effects of single sources of selection in nature is challenging, because environments are often complex with different selective pressures covarying along environmental gradients. For instance, sulfide springs are characterized by high levels of toxic hydrogen sulfide (H2S) and low levels of oxygen in comparison to nearby non-sulfidic streams, which are normoxic. Previous studies on Poecilia mexicana in these sulfide spring systems have focused on the effects of H2S on gene expression, but hypoxia could also impact gene expression. We compared hypoxia tolerance, baseline gene expression of hypoxia related genes, and gene expression after exposure to acute hypoxia across populations from non-sulfidic and sulfidic habitats to make inferences about how these fish survive chronic hypoxia. Overall gene expression patterns were strongly separated by geography (Mexico vs. Costa Rica) and habitat type (sulfidic vs. non-sulfidic), while treatment (hypoxic vs. normoxic) explained less variation. While most gene expression responses were population specific, there were also shared gene expression responses between non-sulfidic and sulfidic populations. Additionally, aquatic surface respiration was required for hypoxia tolerance for fish from both habitat types, suggesting ancestral behavioral and gene expression responses to hypoxia. Fish in sulfide springs exhibited increased constitutive expression of many hypoxia related genes, and they also upregulated more hypoxia-related genes in response to acute hypoxia. Hypoxia tolerance was greater in fish from sulfidic sites, highlighting the importance of constitutive differences in gene expression. Our study sheds light on variation in constitutive and plastic hypoxia responses and sets the stage for future studies to consider interactions between hypoxia and H2S.
Dataset DOI: 10.5061/dryad.70rxwdcd9
Description of the data and file structure
This dataset contains hypoxia tolerance and gene expression data for wild Poecilia mexicana in Southern Mexico and Costa Rica.
Files and variables
Missing values are indicated with blank values in all files.
File: Table_S2-Poecilia_mexicana_Annotations_1.csv
Description: This dataset includes protein annotations for genes in the gene expression analysis.
Variables
- gene ID:internal gene id
- gene name:internal gene name
- Subject sequence ID:subject or target (reference genome) sequence id
- E-value:The Expect value (E) is a parameter that describes the number of hits one can expect to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the E value describes the random background noise. For example, an E value of 1 assigned to an alignment means that in a database of the same size one expects to see 1 match with a similar score, or higher, simply by chance.
- Bit score:The bit-score is a rescaled alignment score to indicate the alignment quality, which is independent of the size of the search database. The higher the bit score, the better the alignment is.
- Protein annotations:Protein annotation of the gene
File: 2024CR_ExposureExperiment.xlsx
Description: Summary of exposure treatments and time for Costa Rican fish exposed to hypoxia for the gene expression analysis.
Variables
- Fish: Fish Id
- Population: Fish population (S = sulfidic; NS = non-sulfidic)
- Treatment: Fish Treatment (Control = high oxygen and no sulfide; Sulfidic = hydrogen sulfide, both = low oxygen and hydrogen sulfide, Hypoxic = low oxygen). The Sulfidic and both treatments were not used in these analyses.
- SL = Standard length in mm.
- Time in: Time trial started
- Time out: Time trial ended
- Timehmin =Time in hours and minutes that fish were in exposure treatment
- Time = time in minutes that fish was in exposure treatment
- RNAID =tube number of gill sample in rnalater
- DNAID =tube number of tail in ethanol (note only the gill samples were used in this dataset)
File: CR_Key.xlsx
Description: Key to convert sample names (from field id's) to sample id's (id's used in sequencing) for Costa Rican fish.
Variables
- Sample_Name: fish id
- Sample_ID: sequencing id
File: go_hypoxia_genes.xlsx
Description: Genes annotated to the response to hypoxia Gene Ontology category.
Variables
- Entry: Uniprot accession number
- Reviewed: whether the entry was reviewed or not (all entries were Reviewed)
- Entry Name: Protein abbreviation
- Protein names: protein names and aliases
File: SampleKey_Hypoxia.xlsx
Description: Key to convert sample names (from field id's) to sample id's (id's used in sequencing) for Mexican fish.
Variables
- Files: file name
- Read_names: sequencing id
- Sample_ID: fish sample id
File: Hypoxia_envdata.xlsx
Description: Environmental data for Mexico and Costa rica
Variables
- Drainage: river drainage
- Ecotype: habitat type (sulfidic or non-sulfidic)
- Population: Population name
- Date: Environmental sampling data
- Temperature: Temperature measured in degrees Celsius
- DO: dissolved oxygen measured in mg/L
- Cond: Conductivity measured inMicroSiemens per centimeter
- Ph: water Ph
- Sulfide: sulfide concentrations measured in micromolars
File: counts_matrix_mx.txt
Description: counts matrix for gene expression of Mexican fish
File: counts_matrix_cr.txt
Description: counts matrix for gene expression of Costa Rican fish
File: Hematocrit_Data_Field_2015.xlsx
Description: Hematocrit values collected in Southern Mexico 2015
Variables
- Label: Fish id
- Mass (g): mass of fish measured in g
- Sex: Sex of fish; F = female, M = Male
- Drainage: river drainage, Tac = Tacotalpa, Pich =Pichucalco,
- Sulfur: Habitat type, No =non-sulfidic, Yes =Sulfidic
- Ht = Hematocrit (proportion of red blood cells in blood)
File: 2024Mex_Fieldenvdata.xlsx
Description: Field environmental variables collected in 2024 from Mexico.
Variables
- Drainage: River drainage
- Population: population name
- Date: date that data was collected
- Temperature: temperature in degrees celsius
- DO: dissolved oxygen in mg/L
- Cond:Conductivity measured inMicroSiemens per centimeter
- Ph: water Ph
- Sulfide: sulfide concentrations measured in micromolars
File: Hypoxia_LOE_pilot_datasheets.xlsx
Description: Data from pilot experiment testing the effect of the lid.
Variables
- Date: Date trial was conducted
- Tank: tank that fish were collected from
- Trial: trial number
- Lid: Yes = yes a lid was placed so fish could not reach the surface, N = no lid
- Pop: Population, BON = bonita (non-sulfidic) and PSO = PSO (sulfidic)
- LOE: time until loss of equilibrium (s)
- SL_mm: standard length measured in mm
- Sex: F = female, M = male
- Notes: trial notes, Gravid means a female appeared gravid (though this was not confirmed by dissection)
- Survival: 0 = lost equilibrium, 1 = did not lose equilibrium
File: mexico_2024_LOE.xlsx
Description: Data on time until loss of equilibrium in wild Mexican fish
Variables
- Date: date trial was ran
- Trial: trial number
- Drainage: river drainage
- LOE: time until loss of equilibrium measured in seconds
- Population: fish population
- Habitat_type: fish habitat type (sulfidic or non-sulfidic)
- SL: standard length measured in mm
- Sex: fish sex, F = female, M = male
- Survival:0 = lost equilibrium, 1 = did not lose equilibrium
- Species: fish species, P_mex = Poecilia mexicana, P_therm = Poecilia thermalis, and P_sulph = Poecilia sulphuraria
File: hypdata.csv
Description: Data on fish used for gene expression data. This file is created using the field_RNA_all_genename_2 script and is input for the WGCNA_2.Rmd script.
Variables
- Fish: fish id
- Population: Fish population, VET = vet station, VETS = vet station sulfidic, PSO = pso, BON = bonita, Sulfidic = costa rican sulfidic, Nonsulfidic = costa rican nonsulfidic
- Habitat: Habitat type (sulfidic or nonsulfidic)
- Treatment: exposure treatment: control = normoxic and no sulfide, hypoxic = low oxygen and no sulfide
- SL: standard length measured in mm
- Sample_ID: sample id
- Drainage: river drainge, Pich = Pichucalco, Tac = Tacotalpa
- Samplenumber: sequencing id
- Habitat_Trt: Combination of habitat and treatment ids
- Drain_Habitat_Trt: Combination of habitat, drainage and treatment ids
File: hypcounts.csv
Description: count data created using the field_RNA_all_genename_2 script and is input for the WGCNA_2.Rmd script.
File: 2023_H2S_H_exposuretranscriptomics_Williams.xlsx
Description: Summary of exposure treatments and time for Mexican fish exposed to hypoxia for the gene expression analysis.
Variables
- Fish: Fish Id
- Habitat: Fish habitat type (Sulfidic or Nonsulfidic)
- Pop: Fish population, PSO = pso, BON = Bonita, VET = vet station non sulfidic, VETS = vet station sulfidic
- Treatment: Fish Treatment, C = control (high oxygen and no sulfide), S = sulfidic (hydrogen sulfide and high oxygen), Both = sulfidic and hypoxic (low oxygen and hydrogen sulfide), H = Hypoxic (low oxygen, no hydrogen sulfide). The Sulfidic and both treatments were not used in these analyses.
- Sulfide: NS = non-sulfidic, S = sulfidic
- Oxygen: H = hypoxic, N = normoxic
- DO = dissolved oxygen at the start of the trial measured in mg/L
- SL = Standard length in mm.
- Time in: Time trial started
- Time out: Time trial ended
- ExposureTimehr =Time in hours and minutes that fish were in exposure treatment
- ExposureTimemin = time in minutes that fish was in exposure treatment
- Date: date trial was conducted
- Sampleid =tube number of gill sample in rnalater
- Species: fish species, P_mex = Poecilia mexicana, P_therm = Poecilia thermalis, and P_sulph = Poecilia sulphuraria
Code/software
All data were analyzed in R using the scripts: WGCNA_2.Rmd (WGCNA analysis), survivalanalysismex.Rmd (hypoxia tolerance), hematocrit.Rmd (hematocrit data), field_RNA_all_genename_2.Rmd (differential expression analyses).