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Signatures of selection in natural populations adapted to chronic pollution.

Williams LM, Oleksiak MF - BMC Evol. Biol. (2008)

Bottom Line: Two outlier loci were shared between New Bedford Harbor and Elizabeth River populations, and two different loci were shared between Newark Bay and Elizabeth River populations.In total, 1% to 6% of loci are implicated as being under selection or linked to areas of the genome under selection in three F. heteroclitus populations that reside in polluted estuaries.Shared loci among polluted sites indicate that selection may be acting on multiple loci involved in adaptation, and loci shared between polluted sites potentially are involved in a generalized adaptive response.

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Affiliation: Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA. lmwillia@ncsu.edu

ABSTRACT

Background: Populations of the teleost fish Fundulus heteroclitus appear to flourish in heavily polluted and geographically separated Superfund sites. Populations from three Superfund sites (New Bedford Harbor, MA, Newark Bay, NJ, and Elizabeth River, VA) have independently evolved adaptive resistance to chemical pollutants. In these polluted populations, natural selection likely has altered allele frequencies of loci that affect fitness or that are linked to these loci. The aim of this study was to identify loci that exhibit non-neutral behavior in the F. heteroclitus genome in polluted populations versus clean reference populations.

Results: To detect signatures of natural selection and thus identify genetic bases for adaptation to anthropogenic stressors, we examined allele frequencies for many hundreds of amplified fragment length polymorphism markers among populations of F. heteroclitus. Specifically, we contrasted populations from three Superfund sites (New Bedford Harbor, MA, Newark Bay, NJ, and Elizabeth River, VA) to clean reference populations flanking the polluted sites. When empirical FST values were compared to a simulated distribution of FST values, 24 distinct outlier loci were identified among pairwise comparisons of pollutant impacted F. heteroclitus populations and both surrounding reference populations. Upon removal of all outlier loci, there was a strong correlation (R2=0.79, p<0.0001) between genetic and geographical distance. This apparently neutral evolutionary pattern was not evident when outlier loci were included (R2=0.092, p=0.0721). Two outlier loci were shared between New Bedford Harbor and Elizabeth River populations, and two different loci were shared between Newark Bay and Elizabeth River populations.

Conclusion: In total, 1% to 6% of loci are implicated as being under selection or linked to areas of the genome under selection in three F. heteroclitus populations that reside in polluted estuaries. Shared loci among polluted sites indicate that selection may be acting on multiple loci involved in adaptation, and loci shared between polluted sites potentially are involved in a generalized adaptive response.

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Geographic versus genetic distance. Relationship between genetic distance and geographic distance. Genetic distance was calculated from the mean FST for each pair of populations with (A) and without (B) outlier loci. Circles represent a pairwise comparison of a Superfund versus a reference site, squares represent a Superfund versus a Superfund site comparison, and crosses represent a reference versus a reference site comparison.
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Figure 5: Geographic versus genetic distance. Relationship between genetic distance and geographic distance. Genetic distance was calculated from the mean FST for each pair of populations with (A) and without (B) outlier loci. Circles represent a pairwise comparison of a Superfund versus a reference site, squares represent a Superfund versus a Superfund site comparison, and crosses represent a reference versus a reference site comparison.

Mentions: FST values were calculated for comparisons between all sites with and without outlier loci (Table 4). As would be expected, average FST values were higher in all comparisons before the removal of the outliers. The average FST value (with outliers) between New Bedford Harbor and its reference sites is 0.038, between Newark and its reference sites it is 0.039, and between Elizabeth River and its reference sites it is 0.018. Upon removal of the outliers, average FST values fall to 0.010, 0.016, and 0.011 for New Bedford Harbor, Newark Bay, and Elizabeth River, respectively. These values were plotted against log-ten of geographic distance between sites versus genetic distance [FST/(1 - FST), [73]]. There is no apparent pattern in the distribution of pairwise comparisons corresponding to reference-reference, polluted-reference, or polluted-polluted sites. When outliers were included in the calculation of average FST and plotted against distance, there was no significant linear relationship (R2 = 0.092, p = .0721). Upon removal of the outliers, there was a significant and strong linear relationship (R2 = 0.79, p < 0.0001) between geographic and genetic distance (Fig. 5). Mantel tests that account for multiple comparisons confirmed the significance of both relationships (data not shown). This relationship indicates that 79% of the variability in the neutral genetic distance (without outlier loci) between sites can be explained by geographic distance.


Signatures of selection in natural populations adapted to chronic pollution.

Williams LM, Oleksiak MF - BMC Evol. Biol. (2008)

Geographic versus genetic distance. Relationship between genetic distance and geographic distance. Genetic distance was calculated from the mean FST for each pair of populations with (A) and without (B) outlier loci. Circles represent a pairwise comparison of a Superfund versus a reference site, squares represent a Superfund versus a Superfund site comparison, and crosses represent a reference versus a reference site comparison.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2570689&req=5

Figure 5: Geographic versus genetic distance. Relationship between genetic distance and geographic distance. Genetic distance was calculated from the mean FST for each pair of populations with (A) and without (B) outlier loci. Circles represent a pairwise comparison of a Superfund versus a reference site, squares represent a Superfund versus a Superfund site comparison, and crosses represent a reference versus a reference site comparison.
Mentions: FST values were calculated for comparisons between all sites with and without outlier loci (Table 4). As would be expected, average FST values were higher in all comparisons before the removal of the outliers. The average FST value (with outliers) between New Bedford Harbor and its reference sites is 0.038, between Newark and its reference sites it is 0.039, and between Elizabeth River and its reference sites it is 0.018. Upon removal of the outliers, average FST values fall to 0.010, 0.016, and 0.011 for New Bedford Harbor, Newark Bay, and Elizabeth River, respectively. These values were plotted against log-ten of geographic distance between sites versus genetic distance [FST/(1 - FST), [73]]. There is no apparent pattern in the distribution of pairwise comparisons corresponding to reference-reference, polluted-reference, or polluted-polluted sites. When outliers were included in the calculation of average FST and plotted against distance, there was no significant linear relationship (R2 = 0.092, p = .0721). Upon removal of the outliers, there was a significant and strong linear relationship (R2 = 0.79, p < 0.0001) between geographic and genetic distance (Fig. 5). Mantel tests that account for multiple comparisons confirmed the significance of both relationships (data not shown). This relationship indicates that 79% of the variability in the neutral genetic distance (without outlier loci) between sites can be explained by geographic distance.

Bottom Line: Two outlier loci were shared between New Bedford Harbor and Elizabeth River populations, and two different loci were shared between Newark Bay and Elizabeth River populations.In total, 1% to 6% of loci are implicated as being under selection or linked to areas of the genome under selection in three F. heteroclitus populations that reside in polluted estuaries.Shared loci among polluted sites indicate that selection may be acting on multiple loci involved in adaptation, and loci shared between polluted sites potentially are involved in a generalized adaptive response.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA. lmwillia@ncsu.edu

ABSTRACT

Background: Populations of the teleost fish Fundulus heteroclitus appear to flourish in heavily polluted and geographically separated Superfund sites. Populations from three Superfund sites (New Bedford Harbor, MA, Newark Bay, NJ, and Elizabeth River, VA) have independently evolved adaptive resistance to chemical pollutants. In these polluted populations, natural selection likely has altered allele frequencies of loci that affect fitness or that are linked to these loci. The aim of this study was to identify loci that exhibit non-neutral behavior in the F. heteroclitus genome in polluted populations versus clean reference populations.

Results: To detect signatures of natural selection and thus identify genetic bases for adaptation to anthropogenic stressors, we examined allele frequencies for many hundreds of amplified fragment length polymorphism markers among populations of F. heteroclitus. Specifically, we contrasted populations from three Superfund sites (New Bedford Harbor, MA, Newark Bay, NJ, and Elizabeth River, VA) to clean reference populations flanking the polluted sites. When empirical FST values were compared to a simulated distribution of FST values, 24 distinct outlier loci were identified among pairwise comparisons of pollutant impacted F. heteroclitus populations and both surrounding reference populations. Upon removal of all outlier loci, there was a strong correlation (R2=0.79, p<0.0001) between genetic and geographical distance. This apparently neutral evolutionary pattern was not evident when outlier loci were included (R2=0.092, p=0.0721). Two outlier loci were shared between New Bedford Harbor and Elizabeth River populations, and two different loci were shared between Newark Bay and Elizabeth River populations.

Conclusion: In total, 1% to 6% of loci are implicated as being under selection or linked to areas of the genome under selection in three F. heteroclitus populations that reside in polluted estuaries. Shared loci among polluted sites indicate that selection may be acting on multiple loci involved in adaptation, and loci shared between polluted sites potentially are involved in a generalized adaptive response.

Show MeSH
Related in: MedlinePlus