DOI: 10.5061/dryad.n8pk0p327
title: Fine scale population divergence driven by adaptation to industrial pollutants

description: 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.
description: This dataset contains data from 55 SNPs from <em>Fundulus
 heteroclitus</em> collected from 11 habitats along the shores of
 Massachusetts and Rhode Island (USA). SNPs were assayed using a Fluidigm
 EP-1 system. 
description: # Fine-scale population divergence driven by adaptation to industrial
 pollutants
 [https://doi.org/10.5061/dryad.n8pk0p327](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](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. ###### References: 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.