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Patterns of genetic, phenotypic, and acoustic variation across a chiffchaff ( Phylloscopus collybita abietinus/tristis ) hybrid zone

View Article: PubMed Central - PubMed

ABSTRACT

Characterizing patterns of evolution of genetic and phenotypic divergence between incipient species is essential to understand how evolution of reproductive isolation proceeds. Hybrid zones are excellent for studying such processes, as they provide opportunities to assess trait variation in individuals with mixed genetic background and to quantify gene flow across different genomic regions. Here, we combine plumage, song, mtDNA and whole‐genome sequence data and analyze variation across a sympatric zone between the European and the Siberian chiffchaff (Phylloscopus collybita abietinus/tristis) to study how gene exchange between the lineages affects trait variation. Our results show that chiffchaff within the sympatric region show more extensive trait variation than allopatric birds, with a large proportion of individuals exhibiting intermediate phenotypic characters. The genomic differentiation between the subspecies is lower in sympatry than in allopatry and sympatric birds have a mix of genetic ancestry indicating extensive ongoing and past gene flow. Patterns of phenotypic and genetic variation also vary between regions within the hybrid zone, potentially reflecting differences in population densities, age of secondary contact, or differences in mate recognition or mate preference. The genomic data support the presence of two distinct genetic clades corresponding to allopatric abietinus and tristis and that genetic admixture is the force underlying trait variation in the sympatric region—the previously described subspecies (“fulvescens”) from the region is therefore not likely a distinct taxon. In addition, we conclude that subspecies identification based on appearance is uncertain as an individual with an apparently distinct phenotype can have a considerable proportion of the genome composed of mixed alleles, or even a major part of the genome introgressed from the other subspecies. Our results provide insights into the dynamics of admixture across subspecies boundaries and have implications for understanding speciation processes and for the identification of specific chiffchaff individuals based on phenotypic characters.

No MeSH data available.


Principal component analysis (PCA) illustrating the genetic differentiation across samples from both the allopatric (green = abietinus (A1–A10), yellow = tristis (T1–T10)), and the sympatric (purple = samples from N. sympatric zone (N1–N10), blue = samples from S. sympatric zone (S1–S10)) regions (n = 18,014 SNPs). The map illustrates the geographic locations of samples from each respective group
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ece32782-fig-0003: Principal component analysis (PCA) illustrating the genetic differentiation across samples from both the allopatric (green = abietinus (A1–A10), yellow = tristis (T1–T10)), and the sympatric (purple = samples from N. sympatric zone (N1–N10), blue = samples from S. sympatric zone (S1–S10)) regions (n = 18,014 SNPs). The map illustrates the geographic locations of samples from each respective group

Mentions: Visualization/quantification of genetic differentiation across samples was performed using both Principal component analysis (PCA) and clustering analysis (STRUCTURE) of the high‐stringency SNP data. Figure 3 illustrates the outcome of the PCA analysis using the first and second principal components (PC1 and PC2 explain 17% and 12% of the total variation, respectively). Allopatric abietinus and tristis were well separated from each other, especially along the axis representing principal component 1 and both clustered together in dense groups with the exception of one tristis sample that showed considerable differentiation from other tristis samples, mainly along the PC2 axis. Samples from the sympatric regions clearly occupy an intermediate position between the allopatric individuals, the samples from the northern sympatric zone rather close to the allopatric tristis samples, while the samples from the southern sympatric zone are more scattered with some closer clustering together with allopatric abietinus samples (Figure 3). The STRUCTURE (Pritchard et al., 2000) analysis clearly separated allopatric abietinus and tristis and again, samples from the sympatric zone showed varying degrees of allele sharing to either subspecies indicating that the samples from the sympatric zone have mixed ancestry between abietinus and tristis (Figure 4, K = 2). To test the hypothesis of presence of a third subspecies (fulvescens), we modeled the presence of different numbers of discrete clades within the investigated region (K = 1 to K = 7) and evaluated the number of clades with highest likelihood (Evanno et al. 2005). The results showed that K = 2 had the highest likelihood (Figure 4, detailed results for K = 2 and K = 3 are given), and there was no support for the presence of a distinct clade that differs from abietinus and tristis, again supporting the hypothesis that birds in the sympatric region have a genomic composition with admixed abietinus and tristis alleles (Figure 4).


Patterns of genetic, phenotypic, and acoustic variation across a chiffchaff ( Phylloscopus collybita abietinus/tristis ) hybrid zone
Principal component analysis (PCA) illustrating the genetic differentiation across samples from both the allopatric (green = abietinus (A1–A10), yellow = tristis (T1–T10)), and the sympatric (purple = samples from N. sympatric zone (N1–N10), blue = samples from S. sympatric zone (S1–S10)) regions (n = 18,014 SNPs). The map illustrates the geographic locations of samples from each respective group
© Copyright Policy - creativeCommonsBy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383471&req=5

ece32782-fig-0003: Principal component analysis (PCA) illustrating the genetic differentiation across samples from both the allopatric (green = abietinus (A1–A10), yellow = tristis (T1–T10)), and the sympatric (purple = samples from N. sympatric zone (N1–N10), blue = samples from S. sympatric zone (S1–S10)) regions (n = 18,014 SNPs). The map illustrates the geographic locations of samples from each respective group
Mentions: Visualization/quantification of genetic differentiation across samples was performed using both Principal component analysis (PCA) and clustering analysis (STRUCTURE) of the high‐stringency SNP data. Figure 3 illustrates the outcome of the PCA analysis using the first and second principal components (PC1 and PC2 explain 17% and 12% of the total variation, respectively). Allopatric abietinus and tristis were well separated from each other, especially along the axis representing principal component 1 and both clustered together in dense groups with the exception of one tristis sample that showed considerable differentiation from other tristis samples, mainly along the PC2 axis. Samples from the sympatric regions clearly occupy an intermediate position between the allopatric individuals, the samples from the northern sympatric zone rather close to the allopatric tristis samples, while the samples from the southern sympatric zone are more scattered with some closer clustering together with allopatric abietinus samples (Figure 3). The STRUCTURE (Pritchard et al., 2000) analysis clearly separated allopatric abietinus and tristis and again, samples from the sympatric zone showed varying degrees of allele sharing to either subspecies indicating that the samples from the sympatric zone have mixed ancestry between abietinus and tristis (Figure 4, K = 2). To test the hypothesis of presence of a third subspecies (fulvescens), we modeled the presence of different numbers of discrete clades within the investigated region (K = 1 to K = 7) and evaluated the number of clades with highest likelihood (Evanno et al. 2005). The results showed that K = 2 had the highest likelihood (Figure 4, detailed results for K = 2 and K = 3 are given), and there was no support for the presence of a distinct clade that differs from abietinus and tristis, again supporting the hypothesis that birds in the sympatric region have a genomic composition with admixed abietinus and tristis alleles (Figure 4).

View Article: PubMed Central - PubMed

ABSTRACT

Characterizing patterns of evolution of genetic and phenotypic divergence between incipient species is essential to understand how evolution of reproductive isolation proceeds. Hybrid zones are excellent for studying such processes, as they provide opportunities to assess trait variation in individuals with mixed genetic background and to quantify gene flow across different genomic regions. Here, we combine plumage, song, mtDNA and whole‐genome sequence data and analyze variation across a sympatric zone between the European and the Siberian chiffchaff (Phylloscopus collybita abietinus/tristis) to study how gene exchange between the lineages affects trait variation. Our results show that chiffchaff within the sympatric region show more extensive trait variation than allopatric birds, with a large proportion of individuals exhibiting intermediate phenotypic characters. The genomic differentiation between the subspecies is lower in sympatry than in allopatry and sympatric birds have a mix of genetic ancestry indicating extensive ongoing and past gene flow. Patterns of phenotypic and genetic variation also vary between regions within the hybrid zone, potentially reflecting differences in population densities, age of secondary contact, or differences in mate recognition or mate preference. The genomic data support the presence of two distinct genetic clades corresponding to allopatric abietinus and tristis and that genetic admixture is the force underlying trait variation in the sympatric region—the previously described subspecies (“fulvescens”) from the region is therefore not likely a distinct taxon. In addition, we conclude that subspecies identification based on appearance is uncertain as an individual with an apparently distinct phenotype can have a considerable proportion of the genome composed of mixed alleles, or even a major part of the genome introgressed from the other subspecies. Our results provide insights into the dynamics of admixture across subspecies boundaries and have implications for understanding speciation processes and for the identification of specific chiffchaff individuals based on phenotypic characters.

No MeSH data available.