DOI: 10.5061/dryad.n2z34tn5n
title: Data from: Hypoxia disrupts sex-specific physiology and gene expression leading to decreased fitness in the estuarine sea anemone Nematostella vectensis

description: Coastal seawater hypoxia is increasing in temperate estuaries under global
 climate change, yet it is unknown how low oxygen conditions affect most
 estuarine species. We found that hypoxia has increased since the 1990s in
 an estuary hosting the sea anemone Nematostella
 vectensis (Jacques Cousteau National Estuarine Research Reserve,
 New Jersey, USA). Adult N. vectensis bred from anemones
 collected in this estuary exposed to three consecutive nights of hypoxia
 (dissolved oxygen = 0.5–1.5 mg L−1 for ~12 h night−1) during
 gametogenesis displayed decreased aerobic respiration rates and biomass,
 indicating metabolic disruption. Physiological declines were correlated
 with changes in the expression of genes related to oxygen-dependent
 metabolic processes, many of which are targets of hypoxia-inducible factor
 1α (HIF1α), demonstrating the activity of this transcription factor for
 the first time in this early-diverging metazoan. The upregulation of genes
 involved in the unfolded protein response and endoplasmic reticulum and
 Golgi apparatus homeostasis suggested that misfolded proteins contributed
 to disrupted physiology. Notably, these responses were more pronounced in
 females, demonstrating sex-specific sensitivity that was also observed in
 reproductive outcomes, with declines in female but not male fecundity
 following hypoxia exposure. However, sperm from exposed males had higher
 mitochondrial membrane potential, indicating altered spermatogenesis.
 Further, crosses performed with gametes from hypoxia-exposed adults
 yielded strikingly low developmental success (~2%), yet larvae that did
 develop displayed similar respiration rates and accelerated settlement
 compared to controls. Overall, hypoxia depressed fitness in N.
 vectensis by over 95%, suggesting that even stress-tolerant estuarine
 species may be threatened by coastal deoxygenation.
description: # Data from: Hypoxia disrupts sex-specific physiology and gene expression
 leading to decreased fitness in the estuarine sea anemone Nematostella
 vectensis Dataset includes files for all data associated with experiments.
 ## Data and file structure ### File 1:
 Adult\_combined\_dry\_weight\_data.csv This file is for data pertaining to
 the dry weight of adult sea anemones collected at several time points
 during the experiment. These files have headers, which include: -Treatment
 = dissolved oxygen treatment to which anemones were exposed, either
 normoxia or hypoxia -Day = day of experiment on which data were collected
 -Anemone_dry_weight_g = the dry weight of an individual anemone measured
 in grams ### File 2: Adult\_fecundity\_data.csv This file is for data
 pertaining to the reproductive metrics quantified in anemones upon
 spawning induction. This file contains NA values as a result of combining
 data from female and male animals into a single data sheet. NA values
 indicate sex-specific metrics; for example, rows with data for male
 animals have NAs in the egg counts column as these animals do not produce
 eggs. These files have headers, which include: -Treatment = dissolved
 oxygen treatment to which anemones were exposed, either normoxia or
 hypoxia -Group = culture tub in which anemones resided during the
 experiment; tubs were assigned unique letter codes (A-F) that were kept
 consistent throughout the experiment -Sex = sex (female or male) of
 anemone -Number_within_sex = unique identifier for individual anemones
 -Pan_empty_weight_g = weight in grams of aluminum pan for dry weight
 measurement -Pan_anemone_weight_g = weight in grams of aluminum pan and
 dried anemone tissue -Anemone_dry_weight_g = Pan_anemone_weight_g -
 Pan_empty_weight_g -Water_volume_mL = volume of seawater in mL that was in
 each spawning cup -Egg_count_cells = the number of eggs produced by female
 anemones -Eggs_mg_dry_weight = Egg_count_cells /
 (Anemone_dry_weight_g*1000) -Average_egg_volume_um_3 = average volume (in
 um^3) of eggs produced by a female -Average_egg_volume_um_3_SEM = standard
 error of mean (SEM) for Average_egg_volume_um_3 (used for plotting)
 -Sperm_concentration_cells_mL = concentration of sperm produced by a male
 -Sperm_concentration_M_cells_mL = Sperm_concentration_cells_mL/1000000
 -Sperm_count_M_cells = perm_concentration_M_cells_mL * Water_volume_mL
 -Average_sperm_red_green_ratio = average red to green fluorescence ratio
 for sperm produced by a male, as quantified with JC-1 via flow cytometry
 -Average_sperm_red_green_ratio_SEM = SEM for Average_sperm_red_green_ratio
 -Development_success_percent = percentage of larvae successfully developed
 in cross to which each anemone contributed gametes -Expected_offspring =
 fecundity (egg or sperm count) * Development_success_percent
 -Relative_fitness = relative fitness of each anemone calculated by
 dividing Expected_offspring by median Expected_offspring for normoxia
 group (by sex) ### File 3: Adult\_respiration\_data.csv This file is for
 data pertaining to the respiration rates of adult anemones. These files
 have headers, which include: -Day = day of experiment on which data were
 collected -Treatment = dissolved oxygen treatment to which anemones were
 exposed, either normoxia or hypoxia -Group = culture tub in which anemones
 resided during the experiment; tubs were assigned unique letter codes
 (A-F) that were kept consistent throughout the experiment -Anemone_number
 = unique identifier for individual anemones -Anemone_volume_uL = anemone
 volume in uL determined via water displacement -Well = well of respiration
 plate in which vial containing anemone was placed -Vial_volume_mL = volume
 of wells used for respirometry -Water_volume_mL = Vial_volume_mL -
 (Anemone_volume_uL*1000) -Pan_empty_weight_g = weight in grams of aluminum
 pan for dry weight measurement -Pan_anemone_weight_g = weight in grams of
 aluminum pan and dried anemone tissue -Anemone_dry_weight_g =
 Pan_anemone_weight_g - Pan_empty_weight_g -Respiration_rate_umol_L_min =
 oxygen consumption rate of anemone (within vials)
 -Respiration_rate_umol_min_g = oxygen consumption rate of anemone
 (normalized to dry weight) ### File 4: Adult\_spawning frequency\_data.csv
 This file is for data pertaining to the number of anemones spawned in each
 experimental treatment. These files have headers, which include:
 -Treatment = dissolved oxygen treatment to which anemones were exposed,
 either normoxia or hypoxia -Group = culture tub in which anemones resided
 during the experiment; tubs were assigned unique letter codes (A-F) that
 were kept consistent throughout the experiment -Number_of_animals = number
 in tub -Animals_spawned = number spawned -Spawned_percent =
 Animals_spawned/Number_of_animals*100 ### File 5:
 Development\_success\_data.csv This file is for data pertaining to the
 developmental success of eggs from female anemones. These files have
 headers, which include: -Treatment = dissolved oxygen treatment to which
 anemones were exposed, either normoxia or hypoxia -Group = culture tub in
 which anemones resided during the experiment; tubs were assigned unique
 letter codes (A-F) that were kept consistent throughout the experiment
 -Number_of_eggs = number of eggs placed in culture dish -Number_of_larvae
 = number of larvae successfully developed at 3 days post-fertilization
 -Development_success_percent = Number_of_larvae/Number_of_eggs*100 ###
 File 6: Egg\_size\_data.csv This file is for data pertaining to the sizes
 of eggs produced by female anemones. These files have headers, which
 include: -Treatment = dissolved oxygen treatment to which anemones were
 exposed, either normoxia or hypoxia -Group = culture tub in which anemones
 resided during the experiment; tubs were assigned unique letter codes
 (A-F) that were kept consistent throughout the experiment
 -Anemone_number_in_group = unique identifier for individual anemones
 -Egg_length_cm = egg length in cm -Egg_width_cm = egg width in cm
 -Egg_volume_um_3 = egg volume in um^3 calculated from length and width ###
 File 7: Larval\_respiration\_data.csv This file is for data pertaining to
 the respiration rates of larvae. These files have headers, which include:
 -Treatment = dissolved oxygen treatment to which anemones were exposed,
 either normoxia or hypoxia -Respiration_rate_umol_L_min = respiration rate
 of larvae in umol/L/min -Protein_mg = protein content of larvae
 -Water_volume_L = volume of water for wells in which respiration rates
 were measured -Respiration_rate_nmol_min_mg = respiration rate of larvae
 normalized to protein ### File 8: Settlement\_data.csv This file is for
 data pertaining to larval settlement rates. These files have headers,
 which include: -Treatment = dissolved oxygen treatment to which anemones
 were exposed, either normoxia or hypoxia -Days_post_fertilization = day
 after fertilization on which data were collected -Replicate = technical
 replicate of group of 10 larvae (unique number 1-4) -Number_of_larvae =
 number of larvae put in dishes for settlement trials -Number_of_juveniles
 = number of animals settled into juveniles on each day -Percent_juveniles
 = Number_of_juveniles/Number_of_larvae*100 ### File 9:
 Sperm\_MMP\_data.csv This file is for data pertaining to sperm
 mitochondrial membrane potential (MMP) as determined via JC-1 dye and flow
 cytometry. These files have headers, which include: -Treatment = dissolved
 oxygen treatment to which anemones were exposed, either normoxia or
 hypoxia -Group = culture tub in which anemones resided during the
 experiment; tubs were assigned unique letter codes (A-F) that were kept
 consistent throughout the experiment -Anemone_number_in_group = unique
 identifier for individual anemones -Red_to_green_ratio = ratio of red to
 green JC-1 fluorescence for individual sperm cells ### Files 10-12:
 Term2name\_, gene\_, and ont\_list.csv These files are for useful
 information about genes used for RNAseq data analysis. These files have
 headers, which include: -term = gene ontology term code -name = name of
 gene ontology term -gene = gene with each ontology term -ontology = type
 of gene ontology term (biological process, molecular function, or cellular
 component) ### File 13: Summary\_count\_table.txt This is the summary
 count table generated from the RNA sequencing data raw reads (see
 publication for details) ## Sharing/Access information Links to other
 publicly accessible locations of the data: * NA Data was derived from the
 following sources: * NA ## Code/Software ### Files 1 and 2: Nematostella
 hypoxia repro code.Rmd and .pdf These files contain code (in Rmarkdown and
 PDF formats) that was used to analyze and generate plots of data. This
 code can be run using the repository files.