Limits...
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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Venn diagram of shared outlier loci among Superfund populations. Shared outlier loci among Superfund population comparisons to both clean reference sites; numbers in the unions of circles represent outlier loci shared between two Superfund populations.
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Figure 4: Venn diagram of shared outlier loci among Superfund populations. Shared outlier loci among Superfund population comparisons to both clean reference sites; numbers in the unions of circles represent outlier loci shared between two Superfund populations.

Mentions: In comparisons of the three Superfund sites and their clean reference sites, twenty-four loci show patterns indicative of selection. The criteria for identifying these selective loci are that they were identified as outliers in pairwise comparisons of each Superfund site population relative to its two reference site populations (polluted versus both references, analyzed separately, i.e. the union of polluted versus reference 1 and polluted versus reference 2) but not in comparisons between the reference site populations. Eighteen of these twenty-four loci were found in the New Bedford Harbor comparisons, four were found in the Newark Bay comparisons, and six were found in the Elizabeth River comparisons (Fig. 3). Four of these loci were shared between two Superfund site populations suggesting conserved mechanisms of adaptation (Fig. 4).


Signatures of selection in natural populations adapted to chronic pollution.

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

Venn diagram of shared outlier loci among Superfund populations. Shared outlier loci among Superfund population comparisons to both clean reference sites; numbers in the unions of circles represent outlier loci shared between two Superfund populations.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Venn diagram of shared outlier loci among Superfund populations. Shared outlier loci among Superfund population comparisons to both clean reference sites; numbers in the unions of circles represent outlier loci shared between two Superfund populations.
Mentions: In comparisons of the three Superfund sites and their clean reference sites, twenty-four loci show patterns indicative of selection. The criteria for identifying these selective loci are that they were identified as outliers in pairwise comparisons of each Superfund site population relative to its two reference site populations (polluted versus both references, analyzed separately, i.e. the union of polluted versus reference 1 and polluted versus reference 2) but not in comparisons between the reference site populations. Eighteen of these twenty-four loci were found in the New Bedford Harbor comparisons, four were found in the Newark Bay comparisons, and six were found in the Elizabeth River comparisons (Fig. 3). Four of these loci were shared between two Superfund site populations suggesting conserved mechanisms of adaptation (Fig. 4).

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