DOI: 10.5061/dryad.q2bvq83kw
title: Raw mass-standardized ionomic data from seven fish species and raw transcriptome sequences for mosquitofish inhabiting the Tar Creek Superfund Site in OK, USA

description: Our understanding of the mechanisms mediating the resilience of organisms
 to environmental change remains lacking. Heavy metals negatively affect
 processes at all biological scales, yet organisms inhabiting contaminated
 environments must maintain homeostasis to survive. Tar Creek in Oklahoma,
 USA, contains high concentrations of heavy metals and an abundance of
 Western mosquitofish (Gambusia affinis), though several fish species
 persist at lower frequency. To test hypotheses about the mechanisms
 mediating the persistence and abundance of mosquitofish in Tar Creek, we
 integrated ionomic data from seven resident fish species and
 transcriptomic data from mosquitofish to test hypotheses about the
 mechanisms mediating the persistence of mosquitofish in Tar Creek. We
 predicted that mosquitofish minimize uptake of heavy metals more than
 other Tar Creek fish inhabitants and induce transcriptional responses to
 detoxify metals that enter the body, allowing them to persist in Tar Creek
 at higher density than species that may lack these responses. Tar Creek
 populations of all seven fish species accumulated heavy metals, suggesting
 mosquitofish cannot block uptake more efficiently than other species. We
 found population-level gene expression changes between mosquitofish in Tar
 Creek and nearby unpolluted sites. Gene expression differences primarily
 occurred in the gill, where we found upregulation of genes involved with
 lowering transfer of metal ions from the blood into cells and mitigating
 free radicals. However, many differentially expressed genes were not in
 known metal response pathways, suggesting multifarious selective regimes
 and/or previously undocumented pathways could impact tolerance in
 mosquitofish. Our systems-level study identified well characterized and
 putatively new mechanisms that enable mosquitofish to inhabit heavy
 metal-contaminated environments.
description: The data comprising this dataset was collected in a two-part
 field experiment in the Tar Creek Superfund site in Ottawa County,
 Oklahoma, USA from 2017-2018. In the first experiment, we sampled the fish
 communities of Tar Creek (polluted) and a nearby unpolluted reference
 watershed (Coal Creek), and measured whole-body elemental composition of
 numerous biologically relevant elements (i.e., ionomes). In the second
 experiment, we sampled populations of Western mosquitofish
 (<em>Gambusia affinis</em>) in Tar Creek and in two unpolluted
 references (Coal Creek and Little Elm Creek), and generated transcriptomes
 to understand patterns of gene expression variation related to chronic
 heavy metal exposure. The ionomic dataset was obtained
 by digesting dried fish specimens in a 2:1 mixture of trace metal grade
 HNO<sub>3</sub> and
 H<sub>2</sub>O<sub>2</sub> for analysis using an
 inductively coupled plasma optical emission spectrometer (ICP-OES),
 providing raw absolute abundances (in ug) of all elements surveyed. We
 then mass-standardized this data to obtain concentrations of each element
 in ug/mg of dried tissue, which is the data presented and archived in this
 dataset, under the "Ionomics_Data" tab. The
 transcriptomic dataset was obtained by extracting RNA from gills, liver,
 and brain tissues of female <i>G. affinis</i>, and reverse
 transcribing it into cDNA, resulting in transcriptomes containing
 paired-end 101 bp raw reads. Raw transcriptomes are archived on GenBank
 (BioProject accession: PRJNA707024). We then trimmed low quality reads and
 adapter sequences and removed reads shorter than 50 bp. To reduce bias due
 to differences in library sizes, we randomly subsampled reads from the
 samples with abnormally high read counts. These remaining reads were
 mapped to the <em>Xiphophorus maculatus </em>reference genome
 and we generated a count matrix of read counts for each of the 27,266
 genes found in each sample. The raw counts matrix is presented and
 archived in this dataset in columns A-BE of the
 "Gene_Exp_Counts_Matrix" tab. We also used likelihood ratio
 tests to compare expression of each gene between Tar Creek and both
 unpolluted sites, and the results and pertinent statistics for the LRT for
 each gene are also presented in this dataset
 ("Gene_Exp_Counts_Matrix" tab) in columns BF-CI.
description: A README file has been uploaded as a separate tab along with the
 ionomic and transcriptomic data. Please refer to this file for
 explanations of both datasets.