Fine scale population divergence driven by adaptation to industrial pollutants
Data files
Aug 13, 2024 version files 219.97 KB
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Dryad.July2024.xlsx
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README.md
Abstract
The federal Superfund site at New Bedford Harbor (Massachusetts, USA) is an example of an environment where pollution levels rose quickly and dramatically. Industrial waste containing polychlorinated biphenyls, heavy metals, and other organic pollutants was dumped into the harbor in the mid-20th century. The mummichog (Fundulus heteroclitus) is a widely distributed fish typically susceptible to polychlorinated biphenyl toxicity. However, the population in New Bedford Harbor is one of several that have evolved the ability to tolerate this category of toxicants. Constituents of the aryl hydrocarbon receptor system are linked to this adaptive pollution tolerance. Our population genetic analysis of 444 mummichogs from Massachusetts and Rhode Island estuaries using 55 SNP loci suggests that F. heteroclitus near New Bedford Harbor has large populations and restricted but meaningful levels of gene exchange among adjacent habitats. When comparing polluted to cleaner sites, we find strong evidence of genetic differentiation at a small geographic scale. Populations at the two most polluted sites form a genetically distinct cluster. Much of this differentiation is driven by allele frequency differences at loci associated with the aryl hydrocarbon receptor system. While allele frequencies at loci associated with pollution tolerance vary between clean and polluted habitats, putatively adaptive alleles are present at low frequencies elsewhere in our study area.
README: Fine-scale population divergence driven by adaptation to industrial pollutants
https://doi.org/10.5061/dryad.n8pk0p327
We analyzed 55 SNPs in 444 Fundulus heteroclitus collected from 11 habitat patches along the southern shores of Massachusetts and Rhode Island. These include habitats within the highly polluted Superfund site in and around New Bedford Harbor. Fish in these habitats have been shown to have evolved to tolerate high levels of polychlorinated biphenyl (PCB) pollution (Nacci et al, 1999). Several of the SNPs surveyed are within loci hypothesized to be important in PCB tolerance.
Nacci, D., et al. "Adaptations of wild populations of the estuarine fish Fundulus heteroclitus to persistent environmental contaminants." Marine Biology 134 (1999): 9-17.
Description of the data and file structure
Data are shared as a tabbed Microsoft Excel file.
Tab 1
contains raw data in GenAlEx format (Peakall and Smouse, 2006).
Collection sites are as follows:
Site Abbreviation | Latitude | Longitude |
---|---|---|
Jer | 41.378633 | -71.520329 |
Wan | 41.42546 | -71.493284 |
Mid | 41.457453 | -71.452356 |
Hor | 41.509331 | -71.055776 |
Slo | 41.540297 | -70.97305 |
Apo | 41.5836641 | -70.950807 |
Bch | 41.655335 | -70.914554 |
NBH | 41.674565 | -70.912979 |
Hak | 41.63155 | -70.883071 |
Win | 41.596777 | -70.861887 |
Mat | 41.648567 | -70.824761 |
Locus names (eg AHR2_792) are defined in Tab 2. Additional details are available in the main publication https://doi.org/10.1093/jue/juae016
Tab 2
contains information on individual single nucleotide polymorphism (SNP) loci, including the sequence of adjacent DNA, chromosome position (when known), and links to GenBank records. Records have been color-coded to reflect potential changes in coding sequences (Synonymous substitutions are green, Missence substitutions are yellow, and Nonsense mutations are orange.
Tab 3
contains primer/probe sequences for Fluidigm genotyping.
ASP refers to Allele-Specific Primers. These are oligonucleotides that match with one of the two SNP variants
LSP refers to Locus Specific Primers that recognize conserved flanking regions near the SNP
STA refers to Specific Target Amplification - these are primer sets used to pre-amplify weak DNA samples or those from non-model organisms.
Peakall, R. O. D., and Peter E. Smouse. "GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research." Molecular ecology notes 6.1 (2006): 288-295.
Methods
This dataset contains data from 55 SNPs from Fundulus heteroclitus collected from 11 habitats along the shores of Massachusetts and Rhode Island (USA). SNPs were assayed using a Fluidigm EP-1 system.