Evolution of Darwin’s finches and their beaks revealed by genome sequencing

Journal name:
Nature
Volume:
518,
Pages:
371–375
Date published:
DOI:
doi:10.1038/nature14181
Received
Accepted
Published online

Abstract

Darwin’s finches, inhabiting the Galápagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin’s finch species and two close relatives. Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis), a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin’s finches and, thereby, to an expanded utilization of food resources.

At a glance

Figures

  1. Sample locations and phylogeny of Darwin/'s finches.
    Figure 1: Sample locations and phylogeny of Darwin’s finches.

    a, Geographical origin of samples; the letter after the species name is the abbreviation used for geographical origin. The map is modified from ref. 30. b, Maximum-likelihood trees based on all autosomal sites; all nodes having full local support on the basis of the Shimodaira–Hasegawa test are marked by asterisks. The colour code for groups of species applies to both panels. Taxa that showed deviations from classical taxonomy are underscored.

  2. Population history.
    Figure 2: Population history.

    a, Dating the nodes (in thousands of years) with confidence intervals (when applicable) in the phylogeny on the basis of divergence corrected for coalescence in ancestral populations; the topology is the representation of the inferred species tree from Fig. 1b. b, ABBA–BABA analysis of G. magnirostris, G. difficilis from Wolf and Pinta, and L. noctis. Number of sites supporting different trees is indicated both as a percentage and as actual numbers. The D statistic and corresponding Holm–Bonferroni-corrected P value are given for testing the null hypothesis of symmetry in genetic relationships. Finch heads are reproduced from ref. 5. How and Why Species Multiply: The Radiation of Darwin's Finches by Peter R. Grant & B. Rosemary Grant. Copyright © 2008 Princeton University Press. Reprinted by permission.

  3. A major locus controlling beak shape.
    Figure 3: A major locus controlling beak shape.

    a, Genome-wide FST screen comparing G. magnirostris and G. conirostris (Española) having blunt beaks with G. conirostris (Genovesa) and G. difficilis (Wolf) having pointed beaks. The y axis represents ZFST values. b, Nucleotide diversities in the ALX1 region. The 240-kb region showing high homozygosity in blunt-beaked species is highlighted. Red and blue colours in bd refer to blunt and pointed beak haplotypes, respectively. c, Neighbour-joining haplotype tree of ALX1 region. Haplotypes originating from heterozygous birds (see text) are indicated in yellow. Estimated time since divergence (± confidence interval) of blunt and pointed beak haplotypes are given in thousands of years. d, Upper panel: genotypes at 335 SNPs showing complete fixation between ALX1 haplotypes associated with blunt (B) and pointed (P) beaks. d, Middle panel: classification of alleles associated with blunt beaks at the 335 SNPs as derived or ancestral on the basis of allelic state in the outgroup. d, Lower panel: PhastCons35 scores (on the basis of human, mouse and finch alignments) for the 335 SNP sites. TFBS, transcription factor binding sites. e, Linear regression analysis of beak-shape scores among G. fortis individuals on Daphne Major Island classified according to ALX1 genotype; distribution of pointedness in each class is shown as a boxplot; n = 62; F = 17.7, adjusted R2 = 0.22. Differences in six individual body and beak size traits were not significant (all P > 0.05).

  4. Read depth.
    Extended Data Fig. 1: Read depth.

    Average read depth in all 120 samples of Darwin’s finches and outgroup species.

  5. Genetic diversity among Darwin/'s finches.
    Extended Data Fig. 2: Genetic diversity among Darwin’s finches.

    Heat map illustrating the proportion of shared and fixed polymorphisms among Darwin’s finches and outgroup species.

  6. Network tree for the Darwin/'s finches on the basis of all autosomal sites.
    Extended Data Fig. 3: Network tree for the Darwin’s finches on the basis of all autosomal sites.

    Taxa that showed deviations from classical taxonomy are underscored. Finch heads are reproduced from ref. 5. How and Why Species Multiply: The Radiation of Darwin's Finches by Peter R. Grant & B. Rosemary Grant. Copyright © 2008 Princeton University Press. Reprinted by permission.

  7. Taxonomy and rate of speciation.
    Extended Data Fig. 4: Taxonomy and rate of speciation.

    a, Morphological variation among populations of ground finch (Geospiza) species, scandens, fuliginosa and three others, acutirostris, difficilis and septentrionalis, that were formerly classified as a single species (difficilis). Data are from refs 56, 57, and from ref. 58 for weights and measures of difficilis on Fernandina. b, Morphological variation among populations of G. scandens, conirostris, propinqua and magnirostris assessed by multiple discriminant function analysis in JMP version 9. In a discriminant function analysis of the measured variables, all populations were correctly identified to species (−2 log likelihood P = 0.02). Maximum discrimination was achieved by entering three variables in the sequence beak width, beak length and body size (weight or wing). Substituting beak depth for beak width gave the same result. No other variable entered significantly. Data are from ref. 57, except for scandens and magnirostris data from ref. 30. c, Species accumulation on a log scale as a function of time before the present, dating based on mtDNA. Species are expected to accumulate linearly according to a ‘birth–death’ process, eventually declining under a density- (diversity-) dependent mechanism59.

  8. Phylogenies for mtDNA and the sex chromosomes Z and W.
    Extended Data Fig. 5: Phylogenies for mtDNA and the sex chromosomes Z and W.

    a, Tree based on mtDNA sequences. The dating of the nodes and their variances (in thousands of years) is based on the cytochrome b sequences using the fossil-calibrated divergence rate 2.1% per million years for birds46. This tree based on the full mtDNA sequences shows only minor differences compared with previously published trees based only on the cytochrome b sequence6, 9. b, Maximum-likelihood trees based on all Z-linked sites; all nodes having full local support on the basis of the Shimodaira–Hasegawa test are marked by asterisks. c, Tree based on W sequences, only females. Taxa that showed deviations from classical taxonomy are underscored (applies to ac).

  9. ABBA-BABA analysis and demographic history.
    Extended Data Fig. 6: ABBA–BABA analysis and demographic history.

    a, ABBA–BABA analysis of G. magnirostris, G. conirostris on Española and on Genovesa, and with L. noctis as outgroup. b, Comparison of C. olivacea, C. fusca, a pool of all non-warblers, and with L. noctis as outgroup. The number of informative sites supporting the different trees is indicated both as a percentage and as the actual number. The D statistic and corresponding Holm–Bonferroni-corrected P value are also given for testing the null hypothesis of symmetry in genetic relationships. Finch heads are reproduced from ref. 5. c, PSMC analysis21 of all species except the G. difficilis group. d, PSMC analysis of the G. difficilis group.

  10. Sequence conservation of ALX1.
    Extended Data Fig. 7: Sequence conservation of ALX1.

    Amino-acid alignment of the complete ALX1 sequence among different vertebrates. Amino-acid substitutions between ALX1 alleles associated with blunt and pointed beaks are highlighted. The homeobox domain is indicated.

Tables

  1. Phenotypic description of Darwin/'s finches
    Extended Data Table 1: Phenotypic description of Darwin’s finches
  2. Summary of samples of Darwin/'s finches and outgroup species
    Extended Data Table 2: Summary of samples of Darwin’s finches and outgroup species

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Sequence Read Archive

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Author information

  1. These authors contributed equally to this work.

    • Sangeet Lamichhaney &
    • Jonas Berglund

Affiliations

  1. Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden

    • Sangeet Lamichhaney,
    • Jonas Berglund,
    • Markus Sällman Almén,
    • Manfred Grabherr,
    • Alvaro Martinez-Barrio,
    • Marta Promerová,
    • Carl-Johan Rubin,
    • Chao Wang,
    • Neda Zamani,
    • Matthew T. Webster &
    • Leif Andersson
  2. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden

    • Khurram Maqbool &
    • Leif Andersson
  3. Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden

    • Neda Zamani
  4. Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA

    • B. Rosemary Grant &
    • Peter R. Grant
  5. Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA

    • Leif Andersson

Contributions

P.R.G. and B.R.G. collected the material. L.A., P.R.G. and B.R.G. conceived the study. L.A. and M.T.W. led the bioinformatic analysis of data. S.L. and J.B. performed the bioinformatic analysis with contributions from M.S.A., K.M., M.G., A.M.-B., C.-J.R. and N.Z. M.P. and C.W. performed experimental work. L.A., S.L., J.B., B.R.G., P.R.G. and M.T.W. wrote the paper with input from the other authors. All authors approved the manuscript before submission.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to:

The Illumina reads have been submitted to the short reads archive (http://www.ncbi.nlm.nih.gov/sra) under accession number PRJNA263122 and the consensus sequence for the G. fortis mtDNA has been submitted to GenBank under accession number KM891730.

Author details

Extended data figures and tables

Extended Data Figures

  1. Extended Data Figure 1: Read depth. (292 KB)

    Average read depth in all 120 samples of Darwin’s finches and outgroup species.

  2. Extended Data Figure 2: Genetic diversity among Darwin’s finches. (439 KB)

    Heat map illustrating the proportion of shared and fixed polymorphisms among Darwin’s finches and outgroup species.

  3. Extended Data Figure 3: Network tree for the Darwin’s finches on the basis of all autosomal sites. (321 KB)

    Taxa that showed deviations from classical taxonomy are underscored. Finch heads are reproduced from ref. 5. How and Why Species Multiply: The Radiation of Darwin's Finches by Peter R. Grant & B. Rosemary Grant. Copyright © 2008 Princeton University Press. Reprinted by permission.

  4. Extended Data Figure 4: Taxonomy and rate of speciation. (94 KB)

    a, Morphological variation among populations of ground finch (Geospiza) species, scandens, fuliginosa and three others, acutirostris, difficilis and septentrionalis, that were formerly classified as a single species (difficilis). Data are from refs 56, 57, and from ref. 58 for weights and measures of difficilis on Fernandina. b, Morphological variation among populations of G. scandens, conirostris, propinqua and magnirostris assessed by multiple discriminant function analysis in JMP version 9. In a discriminant function analysis of the measured variables, all populations were correctly identified to species (−2 log likelihood P = 0.02). Maximum discrimination was achieved by entering three variables in the sequence beak width, beak length and body size (weight or wing). Substituting beak depth for beak width gave the same result. No other variable entered significantly. Data are from ref. 57, except for scandens and magnirostris data from ref. 30. c, Species accumulation on a log scale as a function of time before the present, dating based on mtDNA. Species are expected to accumulate linearly according to a ‘birth–death’ process, eventually declining under a density- (diversity-) dependent mechanism59.

  5. Extended Data Figure 5: Phylogenies for mtDNA and the sex chromosomes Z and W. (200 KB)

    a, Tree based on mtDNA sequences. The dating of the nodes and their variances (in thousands of years) is based on the cytochrome b sequences using the fossil-calibrated divergence rate 2.1% per million years for birds46. This tree based on the full mtDNA sequences shows only minor differences compared with previously published trees based only on the cytochrome b sequence6, 9. b, Maximum-likelihood trees based on all Z-linked sites; all nodes having full local support on the basis of the Shimodaira–Hasegawa test are marked by asterisks. c, Tree based on W sequences, only females. Taxa that showed deviations from classical taxonomy are underscored (applies to ac).

  6. Extended Data Figure 6: ABBA–BABA analysis and demographic history. (332 KB)

    a, ABBA–BABA analysis of G. magnirostris, G. conirostris on Española and on Genovesa, and with L. noctis as outgroup. b, Comparison of C. olivacea, C. fusca, a pool of all non-warblers, and with L. noctis as outgroup. The number of informative sites supporting the different trees is indicated both as a percentage and as the actual number. The D statistic and corresponding Holm–Bonferroni-corrected P value are also given for testing the null hypothesis of symmetry in genetic relationships. Finch heads are reproduced from ref. 5. c, PSMC analysis21 of all species except the G. difficilis group. d, PSMC analysis of the G. difficilis group.

  7. Extended Data Figure 7: Sequence conservation of ALX1. (1,591 KB)

    Amino-acid alignment of the complete ALX1 sequence among different vertebrates. Amino-acid substitutions between ALX1 alleles associated with blunt and pointed beaks are highlighted. The homeobox domain is indicated.

Extended Data Tables

  1. Extended Data Table 1: Phenotypic description of Darwin’s finches (199 KB)
  2. Extended Data Table 2: Summary of samples of Darwin’s finches and outgroup species (405 KB)

Supplementary information

PDF files

  1. Supplementary Information (275 KB)

    This file contains Supplementary Text and References.

Excel files

  1. Supplementary Table 1 (79 KB)

    This file contains read depth in males and females for the identification of scaffolds from chromosome Z and W. Part a shows read depth in males and females for scaffolds assigned to the Z chromosome. Part b shows read depth in males and females for scaffolds assigned to the W chromosome.

  2. Supplementary Table 2 (59 KB)

    This file contains details from ABBA-BABA analyses of Darwin’s finch populations. P-values are two-sided Holm-Bonferroni corrected.

Additional data