Genomic divergence in a ring species complex

Journal name:
Nature
Volume:
511,
Pages:
83–85
Date published:
DOI:
doi:10.1038/nature13285
Received
Accepted
Published online

Ring species provide particularly clear demonstrations of how one species can gradually evolve into two, but are rare in nature1, 2, 3. In the greenish warbler (Phylloscopus trochiloides) species complex, a ring of populations wraps around Tibet. Two reproductively isolated forms co-exist in central Siberia, with a gradient of genetic and phenotypic characteristics through the southern chain of populations connecting them4, 5, 6. Previous genetic evidence has proven inconclusive, however, regarding whether species divergence took place in the face of continuous gene flow and whether hybridization between the terminal forms of the ring ever occurred7, 8, 9. Here we use genome-wide analyses to show that, although spatial patterns of genetic variation are currently mostly as expected of a ring species, historical breaks in gene flow have existed at more than one location around the ring, and the two Siberian forms have occasionally interbred. Substantial periods of geographical isolation occurred not only in the north but also in the western Himalayas, where there is now an extensive hybrid zone between genetically divergent forms. Limited asymmetric introgression has occurred directly between the Siberian forms, although it has not caused a blending of those forms, suggesting selection against introgressed genes in the novel genetic background. Levels of reproductive isolation and genetic introgression are consistent with levels of phenotypic divergence around the ring, with phenotypic similarity and extensive interbreeding across the southwestern contact zone and strong phenotypic divergence and nearly complete reproductive isolation across the northern contact zone. These results cast doubt on the hypothesis that the greenish warbler should be viewed as a rare example of speciation by distance6, but demonstrate that the greenish warbler displays a continuum from slightly divergent neighbouring populations to almost fully reproductively isolated species.

At a glance

Figures

  1. Spatial patterns of genetic differentiation within the greenish warbler ring species.
    Figure 1: Spatial patterns of genetic differentiation within the greenish warbler ring species.

    a, Bayesian clustering analysis (BCA) of 95 greenish warblers illustrated as a ring corresponding roughly to geography. For each individual, coloured bars indicate the ancestry proportions for each of the five inferred genetic clusters (see also Extended Data Fig. 4). Light grey areas within the ring depict gaps in sampling (see Extended Data Fig. 1 for details). Inner bars indicate mtDNA types according to ref. 4: white bars, western clade; black bars, eastern clade. Coloured diamonds around the ring designate sampling sites. b, Spatial distribution of nuclear genetic variation along the range of P. t. ludlowi (N = 66 birds) suggests an extensive hybrid zone between P. t. viridanus and P. t. trochiloides. Colours correspond to the sampling sites (coloured diamonds) surrounding the BCA plot. c, Geographical variation and evidence for introgression in a set of highly differentiated SNP markers (FST≥0.85) from three different chromosomes (1A, 18 and 19) between western and eastern Siberian greenish warblers, as summarized by principal coordinate analyses (PCA, N = 95 birds). Arrows pinpoint plumbeitarsus individuals clustering with viridanus or showing intermediate genetic characteristics between the main viridanus and plumbeitarsus clusters. d, Genome-wide PCA based on the analysis of 2,334 SNPs in 95 greenish warblers. PC1 explains 58.45% of the variance and PC2 22.07%. P. t. viridanus and P. t. plumbeitarsus are strongly differentiated by both PCs, with other populations genetically intermediate. The two nitidus individuals strongly differentiate from the other western individuals across the third dimension of the PCA (not shown here).

  2. Sampled sites, geographical variation in SNPs and genetic admixtures.
    Extended Data Fig. 1: Sampled sites, geographical variation in SNPs and genetic admixtures.

    a, Geographical distribution of the sites sampled in this study (see also Extended Data Table 1). Colours correspond to the six subspecies of greenish warblers described in ref. 15 (P.t. trochiloides, yellow; ludlowi, green; obscuratus, orange; nitidus, violet; viridanus, blue; plumbeitarsus, red). Greenish warblers coexisting in central Siberia were classified as viridanus or plumbeitarsus according to their mtDNA, which for males was perfectly concordant with their song4. b, Geographic variation in 2,334 SNP markers across 95 greenish warblers as summarized by PCA. Individual birds are depicted as diamonds and colours represent their geographical origin as shown in a. c, Plot of genetic admixture proportions (Q) according to the five genetic clusters inferred by the software STRUCTURE30. Location names are given in the plot. We also indicate whether a particular individual displays a western (W) or eastern (E) mtDNA haplotype according to ref. 4.

  3. Genetic differentiation based on SNP markers increases with corrected geographical distance around the ring.
    Extended Data Fig. 2: Genetic differentiation based on SNP markers increases with corrected geographical distance around the ring.

    See ref. 6 for geographical distance; Mantel’s r = 0.71, P<0.0001. Pair-wise FST values were calculated among those locations where at least 4 individuals were genotyped (N = 8 locations; sites YK, TL, AA, PK, MN, LN, XN and UY, see Extended Data Fig. 1).

  4. Patterns of genetic differentiation among eight sample sites where at least four individuals were genotyped.
    Extended Data Fig. 3: Patterns of genetic differentiation among eight sample sites where at least four individuals were genotyped.

    The thickness of the lines connecting locations is inversely proportional to the FST values between two given locations. Purple lines connect each population with its closest neighbour around the ring. FST pairwise values ranged from 0.034 to 0.303.

  5. Plots of genetic admixture proportions (Q) according to additional values of K.
    Extended Data Fig. 4: Plots of genetic admixture proportions (Q) according to additional values of K.

    Values of Q were inferred by the software STRUCTURE30. Colours are in agreement with those used to label each subspecies at the bottom of this figure.

Tables

  1. Geographic origin of the 135 greenish warblers analysed in the present study
    Extended Data Table 1: Geographic origin of the 135 greenish warblers analysed in the present study
  2. Patterns of genetic diversity for each of the six subspecies of greenish warblers
    Extended Data Table 2: Patterns of genetic diversity for each of the six subspecies of greenish warblers
  3. Number of markers (N) mapping to different avian chromosomes
    Extended Data Table 3: Number of markers (N) mapping to different avian chromosomes

Accession codes

Primary accessions

Sequence Read Archive

References

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Author information

Affiliations

  1. Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada

    • Miguel Alcaide &
    • Darren E. Irwin
  2. Department of Evolutionary Ecology, Estación Biológica de Doñana – CSIC, Americo Vespucio s/n, 41092 Sevilla, Spain

    • Miguel Alcaide
  3. Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA

    • Elizabeth S. C. Scordato &
    • Trevor D. Price
  4. Department of Ecology and Evolutionary Biology, The University of Colorado, Boulder, Colorado 80309, USA

    • Elizabeth S. C. Scordato

Contributions

M.A. and D.E.I. conceived the genomic study. M.A. designed the genomic analysis, and collected and analysed the sequence data. D.E.I., E.S.C.S. and T.D.P. conducted fieldwork. D.E.I. conducted the cline analysis in the southwestern contact zone. All authors contributed to the writing of the manuscript and have read and approved the manuscript.

Competing financial interests

The authors declare no competing financial interests.

Raw Illumina sequencing data have been deposited in the Sequence Read Archive (SRA) under accession numbers SRX472921 and SRX473141. The list of contigs and information concerning the physical location of the SNP markers used in this study, using the zebra finch genome assembly as reference, have been deposited in the Dryad repository (http://doi.org/10.5061/dryad.6kn93).

Author details

Extended data figures and tables

Extended Data Figures

  1. Extended Data Figure 1: Sampled sites, geographical variation in SNPs and genetic admixtures. (549 KB)

    a, Geographical distribution of the sites sampled in this study (see also Extended Data Table 1). Colours correspond to the six subspecies of greenish warblers described in ref. 15 (P.t. trochiloides, yellow; ludlowi, green; obscuratus, orange; nitidus, violet; viridanus, blue; plumbeitarsus, red). Greenish warblers coexisting in central Siberia were classified as viridanus or plumbeitarsus according to their mtDNA, which for males was perfectly concordant with their song4. b, Geographic variation in 2,334 SNP markers across 95 greenish warblers as summarized by PCA. Individual birds are depicted as diamonds and colours represent their geographical origin as shown in a. c, Plot of genetic admixture proportions (Q) according to the five genetic clusters inferred by the software STRUCTURE30. Location names are given in the plot. We also indicate whether a particular individual displays a western (W) or eastern (E) mtDNA haplotype according to ref. 4.

  2. Extended Data Figure 2: Genetic differentiation based on SNP markers increases with corrected geographical distance around the ring. (92 KB)

    See ref. 6 for geographical distance; Mantel’s r = 0.71, P<0.0001. Pair-wise FST values were calculated among those locations where at least 4 individuals were genotyped (N = 8 locations; sites YK, TL, AA, PK, MN, LN, XN and UY, see Extended Data Fig. 1).

  3. Extended Data Figure 3: Patterns of genetic differentiation among eight sample sites where at least four individuals were genotyped. (291 KB)

    The thickness of the lines connecting locations is inversely proportional to the FST values between two given locations. Purple lines connect each population with its closest neighbour around the ring. FST pairwise values ranged from 0.034 to 0.303.

  4. Extended Data Figure 4: Plots of genetic admixture proportions (Q) according to additional values of K. (223 KB)

    Values of Q were inferred by the software STRUCTURE30. Colours are in agreement with those used to label each subspecies at the bottom of this figure.

Extended Data Tables

  1. Extended Data Table 1: Geographic origin of the 135 greenish warblers analysed in the present study (194 KB)
  2. Extended Data Table 2: Patterns of genetic diversity for each of the six subspecies of greenish warblers (66 KB)
  3. Extended Data Table 3: Number of markers (N) mapping to different avian chromosomes (151 KB)

Supplementary information

Excel files

  1. Supplementary Information File 1 (1.5 MB)

    Genotypes of 95 greenish warblers for a selected set of 2,334 SNPs in GenAlex format. Individual IDs are displayed in the first column and SNP marker genotypes are displayed in two columns. Numerical codes and colours represent the four different nucleotide bases (A=101=red; C=102=blue; G=103=yellow; T=104=green). The bottom row indicates the chromosome (using the zebra finch genome assembly28 as reference) where each SNP marker is located.

  2. Supplementary Information File 2 (1.7 MB)

    Genotypes of 4,018 polymorphic SNP markers across the greenish warbler range in a set of individuals sampled from Kyrgyzstan (site AA) to Nepal (site LN) that encompasses the entire sampled range of P.t ludlowi. The file is in GenAlex format, as described in SI File 1.

  3. Supplementary Information File 3 (948 KB)

    Genotypes of greenish warblers for a set of highly differentiated markers (FST >0.85), grouped by chromosome, between viridanus and plumbeitarsus in GenAlex format. P. t. plumbeitarsus individuals with large chunks of DNA introgressing from viridanus are highlighted in yellow. Principal Coordinate Analyses for individual chromosomes are shown in the worksheet labeled as "PCAs". Here, individuals showing mixed ancestry are emphasized with blue squares. The ID of each individual is also given besides each PCA plot. Chromosomes without significant signal of introgression are also included for comparative purposes (e.g. ChrZ, Chr28 and Chr15). The position of each marker, using the zebra finch genome assembly as reference28, is indicated in the worksheet labeled as "Location".

Word documents

  1. Supplementary Information File 4 (164 KB)

    Summary of the descriptive statistics derived from the Bayesian cluster analysis, as in STRUCTURE30, and generated by the program STRUCTURE Harvester32.

Additional data