The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

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Science  20 Jun 2014:
Vol. 344, Issue 6190, pp. 1410-1414
DOI: 10.1126/science.1253226

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  1. Fig. 1 The crow system.

    Illustrations of carrion crow (left) and hooded crow (right). We sampled gene expression data of regrowing feathers from the head and torso, which differ in coloration. The map below shows the European distribution of the carrion crow (dark gray area) and hooded crow (light gray area); the hybrid zone is shown as a black solid line. Sampling locations of this study in Spain (Sp), Germany (Ge), Poland (Po), and Sweden (Sw) are indicated by filled circles (black, carrion crow; gray, hooded crow). Superimposed on the geographical map are the major axes of genetic variation (principal components PC1 and PC2) derived from whole-genome resequencing data from the four populations (black and gray dots, respectively). [Drawings courtesy of Dan Zetterström]

  2. Fig. 2 The genomic landscape of divergence.

    (A) Pairwise genetic differentiation (FST) in 50-kb sliding windows across the genome between carrion crows and hooded crows (top panel), between carrion crow populations (second panel), between hooded crow populations (third panel), and between carrion crows and hooded crows from across the hybrid zone (bottom panel). Alternating colors denote the different chromosomes; and the dotted horizontal lines mark the 99th-percentile FST estimates of autosomes and the Z chromosome, respectively. Red arrows indicate taxon-specific peaks of consecutive elevated FST windows; black arrows highlight outlier peaks that are specific to comparisons with the refugial Spanish population. (B) The largest and most extreme FST peak was located on scaffolds 78 and 60. Plotted within the peak are 81 of 82 total fixed variants (black bars in top panel, ancestral alleles; gray bars, derived hooded crow–specific alleles). (C) Localized phylogenetic patterns within the genome (“cacti”). The majority of the genome exhibits neutral genetic divergence classified as class II cacti (divergent Spanish population or complete admixture). Two cacti display clear separation of carrion crows (black: Spain, solid circles; Germany, open circles) and hooded crows (gray: Sweden, solid circles, Poland, open circles) (class I cacti; fig. S9). Four exemplar gene models associated with the melanogenesis pathway and associated with visual perception are depicted (green blocks and lines represent exons and introns, respectively) along with the regions assigned to class I cacti (blue).

  3. Fig. 3 The functional genomic basis of plumage color differences.

    (A) Photograph of the developmental stage of feather follicles used for gene expression quantification. (B) Percentage of all expressed genes (white) and melanogenesis genes (striped) inferred to be differentially expressed. (C) Schematic overview of the melanogenesis pathway, with genes underexpressed in skin from torso in hooded crows shown in blue, genes overexpressed shown in red (color scale indicates relative change). Genes either not supported by RNA-seq data or expressed at FPKM (fragments per kilobase of exon per million fragments mapped) levels below 1.0 in both hooded and carrion crows are shown as gray boxes. Pathway relationships are shown for transcriptional activation (black double arrows), protein activation (e.g., by phosphorylation) (black single arrows), and transport (gray single arrow, dotted line).

  4. Fig. 4 Characterization of feather melanocytes.

    Immunohistochemistry on feather follicles of carrion crows (upper panel) and hooded crows (lower panel) for one of the melanogenic enzymes (a-Trp1, cyan) differentially expressed in our RNA-seq data confirms differential melanogenesis pathway activity (left column; view on to barbed ridges of whole-mount feather bulges, yellow arrows) but shows no striking differences in melanocyte density (right column; detail of sectioned feather follicle, magenta square). Matched samples from carrion crows and hooded crows were stained in parallel and imaged under identical conditions to ensure comparability. br, barbed ridge; p, pulp. Scale bar, 50 μm. [Drawing courtesy of Kristina Fraune; feather photo from Wikimedia Commons]