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Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees ( Poecile gambeli )

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ABSTRACT

Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation (FST, Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.

No MeSH data available.


Genetic variation among individual mountain chickadees, as illustrated by the first two principal components from a PCA on the genotype covariance matrix. Individuals from different sampling sites are represented by different colours; high and low elevation sites are labelled in the legend with H and L and plotted as triangles and circles, respectively. MR, Mount Rose; RL, Red Lake; SH, Sagehen.
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RSOS170057F2: Genetic variation among individual mountain chickadees, as illustrated by the first two principal components from a PCA on the genotype covariance matrix. Individuals from different sampling sites are represented by different colours; high and low elevation sites are labelled in the legend with H and L and plotted as triangles and circles, respectively. MR, Mount Rose; RL, Red Lake; SH, Sagehen.

Mentions: The first two principal components accounted for 5.77% of the genotypic variation and revealed no evidence that individuals from the six separate sampling sites were more genetically similar to each other than to those from other sites (PERMANOVA R2 = 0.025; F5,145 = 0.742; p = 0.653) (figure 2). In addition, there was no evidence for overall genetic differentiation among high and low elevation sites (PERMANOVA R2 = 0.001; F1,149 = 0.201; p = 0.870). Similarly, pairwise genome-wide FST and Nei's D estimates for samples of chickadees from different sampling sites were consistent with minimal genetic differentiation (mean FST = 0.020, range: 0.010–0.029). Groups of chickadees from high elevation sampling sites did not consistently exhibit significant genetic differentiation from neighbouring low elevation sites, and the genome-wide FST estimates for most contrasts were not significantly different from zero (table 2). Although some FST estimates were statistically larger than zero, the values of these estimates were very small (table 2). Consistent with the absence of genetic structure among sampling sites, geographical distance was unrelated to genetic distance (Mantel R2 = 0.053; p = 0.520; figure 3a) and elevational distance was unrelated to genetic distance (Mantel R2 = 0.002; p = 0.713; figure 3b). Hierarchical analysis of genetic variation using AMOVA partitioned nearly all of the variance within samples (99.5%), with minute proportions attributed to variation among transects (0.49%) and across elevations within transects (0.01%). Based on these analyses, there was no evidence for significant genetic structuring among transects (ϕ = 0.004; p = 0.10) or among different elevations within transects (ϕ = −0.001; p = 0.59). One PC was retained for the DAPC analysis, which found K = 2 as the most likely number of clusters in explaining the data (figure 4). Individuals with high assignment probabilities for each of the two clusters were found at each site and across elevations (figure 4), consistent with a lack of any discernable population structure.Figure 2.


Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees ( Poecile gambeli )
Genetic variation among individual mountain chickadees, as illustrated by the first two principal components from a PCA on the genotype covariance matrix. Individuals from different sampling sites are represented by different colours; high and low elevation sites are labelled in the legend with H and L and plotted as triangles and circles, respectively. MR, Mount Rose; RL, Red Lake; SH, Sagehen.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5383859&req=5

RSOS170057F2: Genetic variation among individual mountain chickadees, as illustrated by the first two principal components from a PCA on the genotype covariance matrix. Individuals from different sampling sites are represented by different colours; high and low elevation sites are labelled in the legend with H and L and plotted as triangles and circles, respectively. MR, Mount Rose; RL, Red Lake; SH, Sagehen.
Mentions: The first two principal components accounted for 5.77% of the genotypic variation and revealed no evidence that individuals from the six separate sampling sites were more genetically similar to each other than to those from other sites (PERMANOVA R2 = 0.025; F5,145 = 0.742; p = 0.653) (figure 2). In addition, there was no evidence for overall genetic differentiation among high and low elevation sites (PERMANOVA R2 = 0.001; F1,149 = 0.201; p = 0.870). Similarly, pairwise genome-wide FST and Nei's D estimates for samples of chickadees from different sampling sites were consistent with minimal genetic differentiation (mean FST = 0.020, range: 0.010–0.029). Groups of chickadees from high elevation sampling sites did not consistently exhibit significant genetic differentiation from neighbouring low elevation sites, and the genome-wide FST estimates for most contrasts were not significantly different from zero (table 2). Although some FST estimates were statistically larger than zero, the values of these estimates were very small (table 2). Consistent with the absence of genetic structure among sampling sites, geographical distance was unrelated to genetic distance (Mantel R2 = 0.053; p = 0.520; figure 3a) and elevational distance was unrelated to genetic distance (Mantel R2 = 0.002; p = 0.713; figure 3b). Hierarchical analysis of genetic variation using AMOVA partitioned nearly all of the variance within samples (99.5%), with minute proportions attributed to variation among transects (0.49%) and across elevations within transects (0.01%). Based on these analyses, there was no evidence for significant genetic structuring among transects (ϕ = 0.004; p = 0.10) or among different elevations within transects (ϕ = −0.001; p = 0.59). One PC was retained for the DAPC analysis, which found K = 2 as the most likely number of clusters in explaining the data (figure 4). Individuals with high assignment probabilities for each of the two clusters were found at each site and across elevations (figure 4), consistent with a lack of any discernable population structure.Figure 2.

View Article: PubMed Central - PubMed

ABSTRACT

Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation (FST, Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.

No MeSH data available.