Schmidt CA , Tambutté E , Venn AA , Zou Z , Castillo Alvarez C , Devriendt LS , Bechtel HA , Stifler CA , Anglemyer S , Breit CP , Foust CL , Hopanchuk A , Klaus CN , Kohler IJ , LeCloux IM , Mezera J , Patton MR , Purisch A , Quach V , Sengkhammee JS , Sristy T , Vattem S , Walch EJ , Albéric M , Politi Y , Fratzl P , Tambutté S , Gilbert PUPA .

DE-FG02-07ER15899 U.S. Department of Energy (DOE), FWP-FP00011135 U.S. Department of Energy (DOE), DE-AC02-05CH11231 U.S. Department of Energy (DOE), DMR-2220274 NSF | Directorate for Mathematical & Physical Sciences | Division of Materials Research (DMR)

	Fig. 1. Identifying the unknown mineral phases.An unknown spectrum, plotted in black, extracted from a 62 nm single pixel at the surface of a coral skeleton, assigned 95% CCHH by analysis with all components. Reference spectra for all phases, amorphous and crystalline, from synthetic minerals are shown in colors and displaced vertically for clarity. Each reference spectrum is overlapped by the unknown single-pixel spectrum. The χ2 value for each fit with 1 component is displayed to the left of each reference spectrum. Gray vertical lines indicate peak positions for the 7 peaks characteristic of CCHH. B An unknown spectrum from a 57 nm single pixel at the surface of a forming nacre tablet, assigned 82% MHC by analysis with all components. Again, χ2 values of each fit are displayed on the left of each reference spectrum. Gray vertical lines indicate peak positions for the 4 MHC characteristic peaks.
	Fig. 2. CCHH on the surface of coral skeleton.CCHH on the surface of a Stylophora pistillata coral skeleton. A, B Grayscale photoelectron image of a coral skeleton (top) with tissue and embedding material (bottom). The box in (B) indicates the region magnified in (A). In both panels, the colored pixels superimposed on the grayscale micrograph are carbonate Myriad Maps (MMs) of nanoscale mineral phases, displaying only pixels that contained 50% or more of each phase, color coded so red = ACCH2O, green = ACC, cyan = CCHH, magenta = MHC, blue = aragonite, with brighter/darker colors corresponding to greater/lower concentration (see color legend). In (B), the aragonite blue pixels are not displayed so the morphology of the skeleton is visible. This area was analyzed in duplicate with consistent results. C Ca L-edge x-ray absorption spectra of 5 calcium carbonate phases, acquired from synthetic reference minerals, used for MMs and color-coded as in (A), (B). The spectra were displaced vertically for clarity. Color blind readers are referred to Supplementary Fig. 12 to see these same data in different colors.
	Fig. 3. CCHH on the surface of coral skeleton and nacre, not on sea urchin spine.A Myriad Map (MM) of coral skeleton from the smooth cauliflower coral Stylophora pistillata. B MM of nacre from the California red abalone Haliotis rufescens. C MM of sea urchin spine from the California purple sea urchin Strongylocentrotus purpuratus. All biominerals are observed in cross-section. The boxes in panels 1 indicate the regions magnified in panels 2 and 3. For all biominerals, the background is a grayscale photoelectron image of the area; the superimposed colored pixels are MMs obtained using 5 component spectra (Fig. 2C, Supplementary Fig. 1). Colored pixels in all panels represent pixels containing more than 50% of the indicated mineral phase, and are color coded according to the color legend in A1. For clarity, blue pixels of aragonite (for coral and nacre) and calcite (for sea urchin spine) are omitted from all panels. They are included in Supplementary Figs. 4–6, where all phases are displayed for all pixels in the first and second acquisition. All three areas were analyzed in duplicate with consistent results.
	Fig. 4. Validation from infrared spectroscopy.Synchrotron Infrared Nano Spectroscopy (SINS) Fourier Transform InfraRed (FTIR) spectra from coral skeletons and synthetic carbonates acquired with 20 nm resolution. The top spectra in (A–D) were acquired from forming coral surfaces, and the best matching spectra from their synthetic counterparts are shown at the bottom. SINS-FTIR spectra acquired from synthetic carbonates, amorphous, metastable crystalline, and stable aragonite are shown in E, compared with pure aragonite extracted from a coral skeleton. All polydimethylsiloxane (PDMS) contaminant peaks are indicated by pink vertical lines and described in more detail in the Methods section.
	Fig. 5. Possible energy landscape leading to the formation of aragonite or calcite biominerals.The landscape includes all phases thus far found during biomineral formation: metastable ACCH2O, ACC, CCHH, MHC, and stable aragonite or calcite. A There are four pathways to crystallization from ACCH2O to a mature aragonite biomineral: direct or through ACC only, the other two pathways include one at a time CCHH or MHC. B In contrast, there are only two pathways from ACCH2O to a mature calcite biomineral, either directly or through ACC. ACCH2O and ACC are isoenergetic43 and most metastable, all other phases are downhill in the order observed in repeat acquisitions in biominerals here (Supplementary Table 5B) and previously in synthetic systems40–43. The color coding is the same as for all spectra and MMs in this work.