Statistical methods and data for: Absence of heterosis for hypoxia tolerance in F1 hybrids of Tigriopus californicus
Creators: name: Deconinck, Aimee
name: Madalone, Olivia
name: Willett, Chris
Publisher: name: Zenodo
Year: 2024
Subjects: Tigriopus californicus
Aquatic hypoxia
generalized structural equation model
Hybridization

description: This data set includes generalized structural equation models (SEM) for the parental populations and hybrid populations in Stata 18, code for figures in R and data in CSV format.  We used SEM over linear regression in order to also generate estimates of the errors and unexplained variance of the midpoint value of the parents.  First, we encoded sex, nuclear genome composition, collection cohort, days in lab after collection, and arena as variables in both models.  For the hybrid model, we also added terms for mitochondrial genome and interaction terms between sex and nuclear genome composition because we observed a different trend in sex differences for one population.  Separate SEM equations were necessary since parental populations were perfectly colinear with mitochondrial type, whereas F1 hybrids were not.  Since observations were grouped by arena and trial, we utilized a clustered standard error calculator when combining both models to allow for different variance between populations.  After, we tested the linear combinations of the means to determine if F1 hybrids performed significantly different from the midpoint value of the two parental populations. By using the estimates from the SEM, we were able to include the estimated error from the models into the equation as well.  Lastly, we tested the linear combinations of the means to determine if the reciprocal crosses of F1 hybrids performed significantly differently from each other.
description: Funding provided by: National Science FoundationROR ID: https://ror.org/021nxhr62Award Number: IOS-2029156
Funding provided by: National Science FoundationROR ID: https://ror.org/021nxhr62Award Number: IOS-1555959
description: Copepods were collected from four locations along the California coastline in December 2019 and August 2021 under collection permits S-192510001-19262-001 and S-192510001-21127-001. All copepods were then transported to the University of North Carolina at Chapel Hill where they were maintained for experiments.  Gravid females from each population were transferred to petri dishes with artificial sea water (ASW) and stored in a 12L:12D light cycle at 20°C for at least one month (equivalent to one generation) prior to testing.  Salinity was adjusted to 35 ppt, and ground commercial fish flakes, which served as food, were added ad libitum every other week. F1 hybrids were generated by placing virgin females of one population with virgin males from a second population. Copepods were grouped by sex and population then placed in aggregates of 5 into arenas of a water bath.  Temperature was maintained at 20°C by a cooling tower that circulated chilled water through the water bath, and the water bath was kept inside a custom-built glove box.  An air stone placed in the water bath was used to deliver gas into the water continuously.  Nitrogen gas was delivered to the water bath until the dissolved oxygen level reached 0.05 mg/L or less and maintained for 20 hours, then atmospheric air was delivered for 10 hours.  At the end of the assay, copepods were prodded gently with a needle probe to prompt a swimming response, and, if copepods did not swim away, they were assumed to be dead. After each assay, all copepods were sacrificed, individually lysed, and genotyped.  After lysis, a portion of the mitochondrial DNA was amplified via polymerase chain reaction (PCR) using population specific primers.  Any confirmed heteroplasmic individuals were excluded from further analysis.