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Adaptive and neutral markers both show continent ‐ wide population structure of mountain pine beetle ( Dendroctonus ponderosae )

View Article: PubMed Central - PubMed

ABSTRACT

Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single‐nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range‐wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.

No MeSH data available.


Related in: MedlinePlus

STRUCTURE and discriminant analysis of principal components plots of North American Dendroctonus ponderosae populations for K = 3–5 using putatively adaptive loci, neutral loci, and both adaptive and neutral loci combined. Regions underlined below represent: (A) northern Canada; (B) southern Canada; (C) Idaho, Montana, and Washington; (D) Oregon, California, and Nevada; (E) Utah and Wyoming; and (F) Arizona and South Dakota. Stars indicate Whistler and Manning Park.
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ece32367-fig-0002: STRUCTURE and discriminant analysis of principal components plots of North American Dendroctonus ponderosae populations for K = 3–5 using putatively adaptive loci, neutral loci, and both adaptive and neutral loci combined. Regions underlined below represent: (A) northern Canada; (B) southern Canada; (C) Idaho, Montana, and Washington; (D) Oregon, California, and Nevada; (E) Utah and Wyoming; and (F) Arizona and South Dakota. Stars indicate Whistler and Manning Park.

Mentions: In each data set (combined, neutral and adaptive), STRUCTURE analysis showed K = 2 as optimal, separating northern Canadian populations from the southern Canadian and US populations. All randomized data sets reflected this optimal K = 2. STRUCTURE analysis at K = 3 for each of the data sets also distinguished the populations from South Dakota, Arizona, and part of Colorado (Fig. 2: blue), while K = 4 showed clustering of western USA from the remaining US populations in both the neutral and adaptive data sets (Fig. 2: orange and Fig. S1). At K = 4 in the neutral and combined data sets, beetles from Manning Park and Whistler in British Columbia clustered with MPB populations along the west coast USA (Oregon, California, and Nevada: orange). For adaptive SNPs, population groupings are less distinct in each plot, and although some genetic differentiation of west coast US populations can be seen, adaptive SNPs did not identify the Manning Park and Whistler populations as a separate cluster. Further analysis (K = 5) did not differentiate US Rocky Mountain populations (Colorado, Wyoming, and Nevada: pink) from the remaining US populations.


Adaptive and neutral markers both show continent ‐ wide population structure of mountain pine beetle ( Dendroctonus ponderosae )
STRUCTURE and discriminant analysis of principal components plots of North American Dendroctonus ponderosae populations for K = 3–5 using putatively adaptive loci, neutral loci, and both adaptive and neutral loci combined. Regions underlined below represent: (A) northern Canada; (B) southern Canada; (C) Idaho, Montana, and Washington; (D) Oregon, California, and Nevada; (E) Utah and Wyoming; and (F) Arizona and South Dakota. Stars indicate Whistler and Manning Park.
© Copyright Policy - creativeCommonsBy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC5016649&req=5

ece32367-fig-0002: STRUCTURE and discriminant analysis of principal components plots of North American Dendroctonus ponderosae populations for K = 3–5 using putatively adaptive loci, neutral loci, and both adaptive and neutral loci combined. Regions underlined below represent: (A) northern Canada; (B) southern Canada; (C) Idaho, Montana, and Washington; (D) Oregon, California, and Nevada; (E) Utah and Wyoming; and (F) Arizona and South Dakota. Stars indicate Whistler and Manning Park.
Mentions: In each data set (combined, neutral and adaptive), STRUCTURE analysis showed K = 2 as optimal, separating northern Canadian populations from the southern Canadian and US populations. All randomized data sets reflected this optimal K = 2. STRUCTURE analysis at K = 3 for each of the data sets also distinguished the populations from South Dakota, Arizona, and part of Colorado (Fig. 2: blue), while K = 4 showed clustering of western USA from the remaining US populations in both the neutral and adaptive data sets (Fig. 2: orange and Fig. S1). At K = 4 in the neutral and combined data sets, beetles from Manning Park and Whistler in British Columbia clustered with MPB populations along the west coast USA (Oregon, California, and Nevada: orange). For adaptive SNPs, population groupings are less distinct in each plot, and although some genetic differentiation of west coast US populations can be seen, adaptive SNPs did not identify the Manning Park and Whistler populations as a separate cluster. Further analysis (K = 5) did not differentiate US Rocky Mountain populations (Colorado, Wyoming, and Nevada: pink) from the remaining US populations.

View Article: PubMed Central - PubMed

ABSTRACT

Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single‐nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range‐wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.

No MeSH data available.


Related in: MedlinePlus